Add functionality from PR #8 by amason30 · Pull Request #9 · mums2/mpactr

amason30 · 2024-06-18T12:41:55Z

Needed to add features such as:

copy
mpactr object print statement
multiple group filtering

So they can be added to the vignette/website.

* Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs

* 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>

* 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>

* 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>

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>

* 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>

* 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>

* 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>

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>

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>

* 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…

* 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…

* 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…

* 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…

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 *…

* 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…

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 …

* 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 …

* 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 …

* 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 …

Relase bug fixes (#8)

93868dc

* Added functionality for multiple group filters. * Copy functionality added! * Custom print statement added! * RCMD check works! * Fixed incorrect summary after differnt filter runs

amason30 merged commit ba0cda9 into ReleaseArticles Jun 18, 2024

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Add functionality from PR #8 #9

Add functionality from PR #8 #9
amason30 merged 1 commit intoReleaseArticlesfrom
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amason30 commented Jun 18, 2024

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