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Merge stable version - some checks failing
add quarto to actions
amason30
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* Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
amason30
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Aug 8, 2024
* Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
GregJohnsonJr
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Aug 8, 2024
commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
amason30
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Aug 8, 2024
* Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
GregJohnsonJr
added a commit
that referenced
this pull request
Aug 8, 2024
* Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems * lintr and pkgdown errors fixed --------- Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
amason30
added a commit
that referenced
this pull request
Aug 8, 2024
* set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> * Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Hot fixes (#20) * Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> * Hot fixes (#21) * Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems * lintr and pkgdown errors fixed --------- Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> * fix pkgdown error for library call Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix pkgdown error to library call * fix pkgdown error for library call --------- Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
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commit c356c4c Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Date: Thu Aug 8 17:16:42 2024 -0400 Update test-coverage.yml commit 66b9cc0 Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Thu Aug 8 16:52:48 2024 -0400 Fix for codecov commit cbb82da Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Thu Aug 8 16:43:34 2024 -0400 Removal of Quarto release and updates to test_coverage. commit 428dc87 Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Date: Thu Aug 8 15:57:37 2024 -0400 Dev (#18) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> * Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Hot fixes (#20) * Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> * Hot fixes (#21) * Squashed commit of the following: commit cb2fed7 Author: Allison R Mason <31289802+amason30@users.noreply.github.com> Date: Thu Aug 8 13:13:46 2024 -0400 Release articles (#19) * Add functionality from PR 16 (#17) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * Release articles (#10) * set up filter article * add basic readme - consider adding background from original program manual * design logo? * switch article to quarto * add functionality for extracting a single filter summary * add check for technical replicates * add documentation for filter_summary * convert prints to cli and add checks for filter functions * add functionality to return a data.table of similar ions for mispicked workflow * add full draft filter article * update vignette builder * add usethis use_articles created .gitignore * initalize website with pkgdown * Relase bug fixes (#8) (#9) * Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> * fix typo to pass RCMD * fix partial group match warning in tests * remove non-exported function documentation * remove non-exported function documentation * add formatted website * demostrate copy and print functionality * add functionality to extract group averages table) * show step by step tree map * update text * return peak table, not a print of peak table * add accessor for cv values, error if cv filter has not been run failing * update accessor names * fix cv accessor test fail by changing name * fix typos * store raw peak table * remove man pages after changing names * set print inside class * Modified the constructor to allow for data.frames and data.tables to be passed through. * get_group_averages should return group averages of the filtered table at any stage * update variable names to be inclusive of data frame as input * add cv plot * show cv plot of cv filtered data only * format cv threshold plot for the article * add option for merging method, all tests pass * Add new method parameter to documentation * Require users to choose a cv_threshold * add new accessors to website * update roxygen version * create an example dataset that has both solvent and media blanks to show filtering both * Add in new example dataset, update filters, and show mutliple group filters * add downstream analysis article * add get_cv_data reference * add articles ignore * figure out how to order articles - does not work * update todo --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix documentation errors in R CMD - check and all tests pass * ensure articles build * add vignette builder * Revert "fix documentation errors in R CMD - check and all tests pass" This reverts commit f40cd27. * changes to pass check * fix documentation warnings * no vignettes to build * add line ending to fix incomplete line warning * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * Pkgdown Fixes (#12) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> * Prep for release (#14) * Created RMD check full for our R package. * Create test-coverage.yml * Create lintr.yml * explain reference semantics sooner to introduce copy_object * run site through github actions * add in website formatting * see if quarto dependency fixes pkgdown namespace error * add quarto depends to website only * removing quarto from suggets cuases error in assigning vignetter builder * Update pkgdown.yaml add quarto to actions * add lines to solve endline error * Update DESCRIPTION * Update pkgdown.yaml, removed white spaces * load library, not load_all * Update _pkgdown.yml * article packages to website needs * Update pkgdown.yaml * dont use vignette builder - render as html * Create pkgdown_quarto.yml * run with default build_site * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * Update pkgdown_quarto.yml * go back to quarto vignette * update todo * start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test * Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * update TODO * Fix for formatter issues! * Alpha numeric fix * add checks for expected meta_data columns Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * reorganize article to explain the example function sooner * remove notes * test coverage is 100 % for all main scripts * reduce size of example metabpscape df - no more CMD note * fix order of articles on website --------- Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for Ubuntu failing test. * does adding project help? * Update pkgdown.yaml most recent example with quarto added * add project file * change qmd to rmd for pkgdown github actions website * Fix for r-cmd checks * Set mimimum R depend for base pipe * Update r.yml * Added a new lintr workflow * Update lintr.yml * Linted, styled the package! * Lintr (#16) * lint and style R dir - need to fix complexity error * lint and style raw data scripts - no errors * update name to snakecase * update manual pages after lint and styling * Fix small typos in filters documentation * Test have been linted! * Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr" This reverts commit 83e6f3e, reversing changes made to 318927f. * fix typos in articles an lint/style * add back typo fixes in filters documentation * fix character limit lintr issue * add an informative error message a filter has already been applied to input data object * add a designated reference semantics article * add copy_object explaination in filters details * fixed code to resolve knitting error * Fix for cyclomatic complexity. * Add in chemistry documentation suggestions * We don't recommend setting bounds to account for 0's in the table * add expanded section for R6 specifics * Link filter article on main page * be consistent with '.' in documentation * Fix typos and add in suggestions * allow https url for data input --------- Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com> --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * remove quarto articles * add filter article with original mpact dataset * remove numeric name requirement and add informative message for group summary * check passed_ions as well, not failed_ions twice * use original mpact data for filter article * update readme with me article link --------- Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * Fix for examples, and fixing lintr issues. * Fixed failed test issues. * Fixes to cli issue and lintr problems * lintr and pkgdown errors fixed --------- Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> * fix pkgdown error for library call Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com> * fix pkgdown error to library call * fix pkgdown error for library call --------- Co-authored-by: amason30 <masonar@umich.edu> Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com> Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
GregJohnsonJr
added a commit
that referenced
this pull request
Aug 9, 2024
commit 61297f5c1ce7f5fca7a7386f38858daf469a891e
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Fri Aug 9 11:24:21 2024 -0400
Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
commit 8c13f5a990d0744dce0b7f69555046cac6fa3438
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:40:24 2024 -0400
fix pkgdown error for library call
commit 54588ab4b5add79a191ace6cc4ef24b81440b99b
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:39:46 2024 -0400
fix pkgdown error to library call
commit 6f5663be6d8e773c12e4939c3edd54053350bd8e
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:38:43 2024 -0400
fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
commit 69bc8fb4c896eba8aec693bf8d6142084e44844e
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:33:15 2024 -0400
Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
commit 6fde45e043ff78e096abcbc040641681d314ba22
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 15:08:50 2024 -0400
Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
GregJohnsonJr
added a commit
that referenced
this pull request
Aug 9, 2024
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
* Squashed commit of the following:
commit 61297f5c1ce7f5fca7a7386f38858daf469a891e
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Fri Aug 9 11:24:21 2024 -0400
Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
commit 8c13f5a990d0744dce0b7f69555046cac6fa3438
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:40:24 2024 -0400
fix pkgdown error for library call
commit 54588ab4b5add79a191ace6cc4ef24b81440b99b
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:39:46 2024 -0400
fix pkgdown error to library call
commit 6f5663be6d8e773c12e4939c3edd54053350bd8e
Author: amason30 <masonar@umich.edu>
Date: Thu Aug 8 15:38:43 2024 -0400
fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
commit 69bc8fb4c896eba8aec693bf8d6142084e44844e
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:33:15 2024 -0400
Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter arti…
GregJohnsonJr
added a commit
that referenced
this pull request
Aug 9, 2024
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to sho…
amason30
added a commit
that referenced
this pull request
Aug 20, 2024
* Dev (#23)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset t…
amason30
added a commit
that referenced
this pull request
Aug 20, 2024
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to sho…
GregJohnsonJr
added a commit
that referenced
this pull request
Nov 6, 2024
commit 953c7a1fea898dd5255d562e22108e11fdfb3932
Author: amason30 <masonar@umich.edu>
Date: Thu Oct 10 16:44:55 2024 -0400
fix error in dev install path
commit 269b1bc2afda90b3498a8ec841d44768a206ee92
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Oct 10 16:38:19 2024 -0400
Fix issue29 (#30)
* ignore vscode configs
* fix issue #29 - we did not accout for case when no ions are merged
commit 74ced34d23773d4b580b7234c66cf6c990569f5f
Merge: a0fe29e 52013d1
Author: amason30 <masonar@umich.edu>
Date: Thu Oct 10 15:18:18 2024 -0400
Merge branch 'main' of https://github.com/mums2/mpactr
commit a0fe29eddc5ec14e9478154a0259b4d20d259b57
Author: amason30 <masonar@umich.edu>
Date: Thu Oct 10 15:18:01 2024 -0400
add form from source
Co-authored-by: Gregory Johnson <GregJohnsonJr@users.noreply.github.com>
commit 52013d1e74c3e213006fce7d9127af1aa3575c30
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Oct 10 15:17:32 2024 -0400
Update issue templates
commit 697e82912697a3ec91fbbef8fa94fdc3de1eb679
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Oct 10 15:10:37 2024 -0400
Update issue templates
commit a9e30123c568f58edd13d2e5997b81db7e89ad81
Author: amason30 <masonar@umich.edu>
Date: Thu Sep 5 16:37:12 2024 -0400
fix CRAN issues - acronyms
commit aceee2a7f314f323b12b231349428bd008666be5
Author: amason30 <masonar@umich.edu>
Date: Tue Sep 3 11:25:55 2024 -0400
update doc
commit e00a9ba1bcea33307a54657b93846db61f4ba8be
Author: amason30 <masonar@umich.edu>
Date: Tue Sep 3 11:24:45 2024 -0400
fix cran pretest issues - updated doi in description and ingnore logo files in build
commit 2dd311741bca18ba76ad0c8f12a729645b6ed259
Author: amason30 <masonar@umich.edu>
Date: Wed Aug 28 10:08:32 2024 -0400
fix website link in readme
commit 085d630ac52fd2d0a33bce9fa3c7769460f0a08f
Author: amason30 <masonar@umich.edu>
Date: Wed Aug 28 10:00:54 2024 -0400
cran 0.1.0 submission docs
commit a9672788c4f4f02eabc5bf60241b2b1041d7d68e
Author: amason30 <masonar@umich.edu>
Date: Wed Aug 28 09:56:09 2024 -0400
Increment version number to 0.1.0
commit a72f2da1b4d59e5b97a4a781db13ba85ec3befbc
Author: amason30 <masonar@umich.edu>
Date: Wed Aug 28 09:45:26 2024 -0400
update github urls
commit 537c6e3e5eccccab4fb31e597ad8b26122ea3e2b
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 27 12:31:42 2024 -0400
update urls
commit 27d62b6f9357559dd7c3f9811fec5b3a6d74aee8
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 17:22:29 2024 -0400
set all actions to run automatically once a week
commit 0e0b8574be926d07be8a528636c4c5f6a7588e03
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 17:13:00 2024 -0400
update todo
commit b79d11c9c4329c004412cb09bc982c9485ce71ef
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 17:11:29 2024 -0400
add status badges and update install instructions
commit b4a45123160c77c511ad5ff5af0e9b3ead1607b6
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 16:58:50 2024 -0400
remove test workflow
commit f1f372976bbf99b385d8c78ae7004e06d31084d7
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 16:54:16 2024 -0400
re-save rda with new package name
commit ee6c93703b562bcf5893b1066bea271723879cc4
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 16:43:56 2024 -0400
does initiating a new workflow post name change remove artifacts?
commit 7d8b78a1459d7ec92a0185de35abc33d7699e018
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 16:29:55 2024 -0400
rname rproj
commit 8a3dcedc7de4898e126a8050cdfcb3e83623776f
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 15:54:10 2024 -0400
add package Rd back
commit 51a5df06911f8dc3fa405149e90ab1fe2b8df59a
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 15:44:08 2024 -0400
make package name all lowercase
commit e54507d0da89cc24df4e344efe1b6aeb6b329da6
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 15:25:18 2024 -0400
report OS checks in cran-comments
commit 999e1df4d0ce7eed2328350d641a4df6271dc985
Author: amason30 <masonar@umich.edu>
Date: Tue Aug 20 15:19:38 2024 -0400
add 0.1.0 entry
commit 41e99ff9208ec593942a598e2cfb867c2d56e300
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Tue Aug 20 15:04:09 2024 -0400
Dev (#27)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
*…
GregJohnsonJr
added a commit
that referenced
this pull request
Mar 12, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown…
GregJohnsonJr
added a commit
that referenced
this pull request
Mar 27, 2025
commit 0e5b25808de6787fab9763a8df3247b4d1b7707c
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date: Thu Mar 13 15:21:11 2025 -0400
License should be corrected now.
commit 7f2957cda99b77c9d9def3bd5b8e127c298151b4
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date: Thu Mar 13 12:10:26 2025 -0400
Fix for license and pkgdown links.
commit 109473c996106701e595eee03b834092a83c8b8a
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date: Wed Mar 12 17:56:38 2025 -0400
Modifying r build ignores and gitignore
commit cfb2938bb229d97db0152a39646846f27ac80abf
Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com>
Date: Wed Mar 12 17:29:30 2025 -0400
Moving Data.table from depends to import (#32)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article …
GregJohnsonJr
added a commit
that referenced
this pull request
Mar 27, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
…
GregJohnsonJr
added a commit
that referenced
this pull request
Mar 28, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
…
GregJohnsonJr
added a commit
that referenced
this pull request
Mar 28, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto …
GregJohnsonJr
added a commit
that referenced
this pull request
Sep 8, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
…
GregJohnsonJr
added a commit
that referenced
this pull request
Sep 8, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
…
GregJohnsonJr
added a commit
that referenced
this pull request
Sep 9, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
…
GregJohnsonJr
added a commit
that referenced
this pull request
Sep 10, 2025
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
* lintr and pkgdown errors fixed
---------
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
* fix pkgdown error for library call
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix pkgdown error to library call
* fix pkgdown error for library call
* Squashed commit of the following:
commit c356c4c222378b1544b94714b8a7921a5f61e0af
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 17:16:42 2024 -0400
Update test-coverage.yml
commit 66b9cc0b29ca42d5bbef9930714cbd75bb886f16
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:52:48 2024 -0400
Fix for codecov
commit cbb82daf1844fd5938fc98648f7cec125f3a3085
Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 16:43:34 2024 -0400
Removal of Quarto release and updates to test_coverage.
commit 428dc87a68615c8f3e4a53e49d2cf75e120bde52
Author: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Date: Thu Aug 8 15:57:37 2024 -0400
Dev (#18)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Hot fixes (#20)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* Pkgdown Fixes (#12)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
* Prep for release (#14)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
* add lines to solve endline error
* Update DESCRIPTION
* Update pkgdown.yaml, removed white spaces
* load library, not load_all
* Update _pkgdown.yml
* article packages to website needs
* Update pkgdown.yaml
* dont use vignette builder - render as html
* Create pkgdown_quarto.yml
* run with default build_site
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* Update pkgdown_quarto.yml
* go back to quarto vignette
* update todo
* start formatter functions for mpactr class construction - tests pass, need to add to the import and constructor functions and test
* Allow users to submit feature tables exported from different tools - need to fix global bindings warning for formatter script
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* update TODO
* Fix for formatter issues!
* Alpha numeric fix
* add checks for expected meta_data columns
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* reorganize article to explain the example function sooner
* remove notes
* test coverage is 100 % for all main scripts
* reduce size of example metabpscape df - no more CMD note
* fix order of articles on website
---------
Co-authored-by: Allison R Mason <31289802+amason30@users.noreply.github.com>
Co-authored-by: amason30 <masonar@umich.edu>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for Ubuntu failing test.
* does adding project help?
* Update pkgdown.yaml
most recent example with quarto added
* add project file
* change qmd to rmd for pkgdown github actions website
* Fix for r-cmd checks
* Set mimimum R depend for base pipe
* Update r.yml
* Added a new lintr workflow
* Update lintr.yml
* Linted, styled the package!
* Lintr (#16)
* lint and style R dir - need to fix complexity error
* lint and style raw data scripts - no errors
* update name to snakecase
* update manual pages after lint and styling
* Fix small typos in filters documentation
* Test have been linted!
* Revert "Merge branch 'lintr' of https://github.com/SchlossLab/mpactR into lintr"
This reverts commit 83e6f3e7c636c9e6254c396842d7e724958662a9, reversing
changes made to 318927f66ed22048a57b3555c26b3a0a8a4073f5.
* fix typos in articles an lint/style
* add back typo fixes in filters documentation
* fix character limit lintr issue
* add an informative error message a filter has already been applied to input data object
* add a designated reference semantics article
* add copy_object explaination in filters details
* fixed code to resolve knitting error
* Fix for cyclomatic complexity.
* Add in chemistry documentation suggestions
* We don't recommend setting bounds to account for 0's in the table
* add expanded section for R6 specifics
* Link filter article on main page
* be consistent with '.' in documentation
* Fix typos and add in suggestions
* allow https url for data input
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* remove quarto articles
* add filter article with original mpact dataset
* remove numeric name requirement and add informative message for group summary
* check passed_ions as well, not failed_ions twice
* use original mpact data for filter article
* update readme with me article link
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* Fix for examples, and fixing lintr issues.
* Fixed failed test issues.
* Fixes to cli issue and lintr problems
---------
Co-authored-by: YoungKrug <31873199+YoungKrug@users.noreply.github.com>
* Hot fixes (#21)
* Squashed commit of the following:
commit cb2fed761b2b92336b585aec7a8a984249a9cbc9
Author: Allison R Mason <31289802+amason30@users.noreply.github.com>
Date: Thu Aug 8 13:13:46 2024 -0400
Release articles (#19)
* Add functionality from PR 16 (#17)
* Created RMD check full for our R package.
* Create test-coverage.yml
* Create lintr.yml
* Release articles (#10)
* set up filter article
* add basic readme - consider adding background from original program manual
* design logo?
* switch article to quarto
* add functionality for extracting a single filter summary
* add check for technical replicates
* add documentation for filter_summary
* convert prints to cli and add checks for filter functions
* add functionality to return a data.table of similar ions for mispicked workflow
* add full draft filter article
* update vignette builder
* add usethis use_articles created .gitignore
* initalize website with pkgdown
* Relase bug fixes (#8) (#9)
* Added functionality for multiple group filters.
* Copy functionality added!
* Custom print statement added!
* RCMD check works!
* Fixed incorrect summary after differnt filter runs
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
* fix typo to pass RCMD
* fix partial group match warning in tests
* remove non-exported function documentation
* remove non-exported function documentation
* add formatted website
* demostrate copy and print functionality
* add functionality to extract group averages table)
* show step by step tree map
* update text
* return peak table, not a print of peak table
* add accessor for cv values, error if cv filter has not been run failing
* update accessor names
* fix cv accessor test fail by changing name
* fix typos
* store raw peak table
* remove man pages after changing names
* set print inside class
* Modified the constructor to allow for data.frames and data.tables to be passed through.
* get_group_averages should return group averages of the filtered table at any stage
* update variable names to be inclusive of data frame as input
* add cv plot
* show cv plot of cv filtered data only
* format cv threshold plot for the article
* add option for merging method, all tests pass
* Add new method parameter to documentation
* Require users to choose a cv_threshold
* add new accessors to website
* update roxygen version
* create an example dataset that has both solvent and media blanks to show filtering both
* Add in new example dataset, update filters, and show mutliple group filters
* add downstream analysis article
* add get_cv_data reference
* add articles ignore
* figure out how to order articles - does not work
* update todo
---------
Co-authored-by: GregJohnson <31873199+YoungKrug@users.noreply.github.com>
Co-authored-by: GregJohnson <YoungKrug@users.noreply.github.com>
* fix documentation errors in R CMD - check and all tests pass
* ensure articles build
* add vignette builder
* Revert "fix documentation errors in R CMD - check and all tests pass"
This reverts commit f40cd276f43874162d8cbad9d251ab7221afd422.
* changes to pass check
* fix documentation warnings
* no vignettes to build
* add line ending to fix incomplete line warning
* explain reference semantics sooner to introduce copy_object
* run site through github actions
* add in website formatting
* see if quarto dependency fixes pkgdown namespace error
* add quarto depends to website only
* removing quarto from suggets cuases error in assigning vignetter builder
* Update pkgdown.yaml
add quarto to actions
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Fixes to the project as we prepare for the release of mpactr!!!