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* start mismatched peaks filter * check mismatched peaks works correctly now, need to add testing for validity * added merge to check_mismatched_peaks, need to test for validity * mpact removes features that have a rowSum of zero, after we implemented that feature we finally finished testing and creating the relational filter. * Pushing through changes to filters * start blank filter with tidy approach, needs refactoring * needed to sum intensities for merged ions in mismatched peaks filter * fixed group filter test, need to add actual test * add mpact data * Completed test for filter blank! Parse ion list will be created next. * Unit test for group averages is complete! * List filter and test have been added! * Added the CV filter test, and cv filtering! * Started to add deconvolution to the filter script. * Code ideas from yesterday. * start tidy-independent approach for filter blank * make rsd its own function * added new filter function without tidy dependences - tests pass * clean up filter blank 3 code * begin non-tidy approach to parse_ions_by_group, would need to change filter_blank_3 and update tests * refactor filter blank with data.table to improve speed and reduce code * The decon filter has been added and works! Test have been created and everything passes as expected. * begin converting all functions to data.table * update tests to take data.table - need to finish converting functions following check_mismatch_peaks * add ideas to convert insource ion to data.table. need to finish this function, merge with tuesday session, and update tests * merged, we need to figure out which functions are the correct ones. * InSourceIons function has been properly refactored! * Stable version of filters is being pushed through! * Added some comments based on what to do next. --------- Co-authored-by: amason30 <masonar@umich.edu>
* Adding some class structures * add expected metadata format csv * split mpactr class structure into separate scipts by class * begin tests for mpactr class * add full test dataset * Good amount of progress restructuring the data. * Separated the methods from the R6 classes! * Test are failing, but summary class has been implemented * all filters successfully built on R6 class structure. need to work on qc-graph class * move tests for methods to their own script * move mpactr class methods tests to their own script * apply list of summaries in logger to filters. successful. all tests pass * We have created a flow for the creation of a QC tree map graph! * Added Basic pipeline for mpactR! * Returning objects instead of csv's in the filter function * TODO list * Made peak_table and meta_data private and added setter/getters --------- Co-authored-by: amason30 <masonar@umich.edu>
* add author and package decription information * initiate raw data for examples * add dataset for examples * add data for examples to inst instead * add initial documentation * add imports * add raw data to build ignore to pass checks * finialize initial documentation - all tests pass
* add author and package decription information * initiate raw data for examples * add dataset for examples * add data for examples to inst instead * add initial documentation * add imports * add raw data to build ignore to pass checks * finialize initial documentation - all tests pass * add accessor functions for peak and metadata tables - stable
* 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>
This reverts commit f40cd27.
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This version passes R CMD check for macOS build |
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This is the first stable version of mpactR with pre-beta and pre-release features and documentation.