v0.3.0

Overview

This release continues to refine the gsm data workflow and QC process in prepararation for a v1 release. Updates include:

• *_Assess() functions now return a list only. Returns strFunctionName, lParams, and lTags, in addition to all data.frames in the pipeline.
• *_Map_Raw() functions now implement a new utility function: is_mapping_valid() for more robust and diagnostic error checking.
• *_Map_Raw() functions now use a single mapping parameter to facilitate all renames and data checks.
• Added a mergeSubjects() function used to merge domain data with subject-level data and provide useful warnings when subjects aren't matched and/or dropped.

What's Changed

• Fix-271: Update AE_Assess() Qualification by @kodesiba in #272
• AE_Assess() refactor assessment data object + update tests by @mattroumaya in #267
• fixes #221 - qc updates for Analyze_Chisq() by @mattroumaya in #262
• Fix 219 chisq unit tests by @mattroumaya in #270
• fix #264 - refactor assessment data object + update tests by @mattroumaya in #274
• Main by @jwildfire in #293
• Fix 283, 282 (pd_assess) and Analyze_Scatter by @dsanders2gilead in #288
• update AE qualification tests for sorting updates to Flag and Summarise by @kodesiba in #295
• fixed issue #289 with %>% arrange(desc(.data$Flag)) to dfFlag and dfS… by @dsanders2gilead in #292
• Changed Assess examples (names of return values) to reflect new bahav… by @dsanders2gilead in #297
• Fix #276 - parameterize all columns and fields for Consent_Map_Raw() by @mattroumaya in #296
• Fix #277, fix #278: parameterize all columns and fields for IE_Map_Raw() + PD_Map_Raw() by @mattroumaya in #299
• fix #220 add unit tests for Analyze_Fisher() by @mattroumaya in #302
• Add standard mergeSubjects function for use in Map_Raw by @jwildfire in #298
• add tests for fix #308 by @mattroumaya in #311
• update qualification tests for fix-20 by @kodesiba in #314
• updated AE expect_error tests to require error message matching by @dsanders2gilead in #313
• Implement lTags across all assessments #20 by @jwildfire in #309
• remove failing test by @mattroumaya in #318
• Qualify PD and update AE qualification by @kodesiba in #315
• Release v0.3.0 by @mattroumaya in #316

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Overview

This release adds assessment visualizations via Visualize_Scatter and Visualize_Count and addresses many minor documentation and testing issues. See below for a full list of Pull requests or see the v0.2 milestone for a full list of resolved issues.

What's Changed

• Fix 172 ae visualize by @mattroumaya in #174
• Update dev version by @jwildfire in #216
• Improve Poisson Analysis Docs and Refactor Summarize by @jwildfire in #213
• Fix 201 qc ae map raw by @dsanders2gilead in #214
• Fix 231 by @mattroumaya in #234
• closes #230 - qc updates for Summarize() by @mattroumaya in #239
• made changes for IE_Map_Raw to handle column mapping arguments, also … by @dsanders2gilead in #195
• Fix 206 207 qc consent by @dsanders2gilead in #238
• closes #229 - qc updates for Flag() by @mattroumaya in #240
• closes #237 - standardize parameter naming conventions by @mattroumaya in #241
• updated PD_Map and PD_Assess per QC standards by @dsanders2gilead in #244
• closes 210 - qc updates for IE_Map_Raw() by @mattroumaya in #245
• closes 227 - qc updates for Analyze_Poisson() by @mattroumaya in #243
• closes #228 - qc updates for Analyze_Wilcoxon() by @mattroumaya in #242
• migrate AE_Assess qualification to new structure by @kodesiba in #250
• closes #252 - bugfix for Visualize_Poisson() by @mattroumaya in #253
• IE_Assess #211 by @dsanders2gilead in #251
• Fix 224 viz wilcoxon by @mattroumaya in #255
• first draft for Visualize_Count() by @mattroumaya in #258
• revert tests by @mattroumaya in #266
• closes #226 - qc updates for Analyze_Fisher() by @mattroumaya in #261
• Release v0.2.0 by @dsanders2gilead in #257

Full Changelog: v0.1.0...v0.2.0

v0.1.0

Summary

This initial release of {gsm} provides data pipeline functionality for 4 assessments:

• Adverse Events via gsm::AE_Assess()
• Protocol Deviations via gsm::PD_Assess()
• Disposition via gsm::Disposition_Assess()
• Inclusion/Exclusion Criteria via gsm::IE_Assess()

What's Changed

• AE + PD migration by @jwildfire in #16
• added utils-pipe.R by @dsanders2gilead in #31
• removed negativeBinomial from documentation by @dsanders2gilead in #30
• made changes and did ad-hoc testing (since no tests yet) by @dsanders2gilead in #32
• Migrate ae pd test code by @dsanders2gilead in #34
• lThreshold or dThreshold was not hooked up in AE_Assess. I hooked th… by @dsanders2gilead in #35
• Add details for vThreshold option in AE and PD by @jwildfire in #42
• removed strPath from AE_Map_raw.R and did some ad-hoc testing on data… by @dsanders2gilead in #44
• made changes to Flag.R to handle strFlagValueColumn. Wasn't able to f… by @dsanders2gilead in #43
• Update Flag() to use tidyverse logic throughout by @jwildfire in #46
• IE migrated and adhoc testing done with randomly selected IE data. IE… by @dsanders2gilead in #47
• Consent migrated, similar to IE changes were made (Consent_Assess use… by @dsanders2gilead in #51
• Fix 10 timeonstudy by @gwu05 in #45
• Update issue templates by @jwildfire in #64
• Add Github actions by @jwildfire in #54
• most tests/error handling completed except those not sure of by @dsanders2gilead in #53
• Fix 12 exposureduration by @gwu05 in #62
• added bindings to tidyverse colnames - fix #69 by @dsanders2gilead in #70
• Fix 52 by @dsanders2gilead in #61
• Fix 59 timeonstudyfor p dmapraw by @dsanders2gilead in #68
• Adds detailed documentation for AE_Assess by @jwildfire in #84
• added ability to set strValueColumn for flag via AE_Assess wrapper by @dsanders2gilead in #85
• AE_Map_Adam now uses tidy syntax by @dsanders2gilead in #81
• PD_Map_Raw appears complete but PD_Assess throws erros when cMethod =… by @dsanders2gilead in #86
• use SUBJID in map_raw by @jwildfire in #95
• Changed TimeOnStudy column to Exposure by @jwildfire in #96
• Fix 91 by @dsanders2gilead in #98
• refactored Consent_Map_Raw and Consent_Assess to use new column namin… by @dsanders2gilead in #100
• Fix 90 input data doc by @dsanders2gilead in #99
• Feature: PR and Issue Templates by @kodesiba in #109
• Issue and Pull Request Template Updates by @kodesiba in #111
• added documentation + example for TreatmentExposure as well as tests.… by @dsanders2gilead in #105
• clone/install clindata #101 by @jwildfire in #115
• Refactor Analyze Poisson using broom by @jwildfire in #114
• Fix 107 ae assessment qualification docs by @kodesiba in #122
• Fix 102 ae map raw clindata tests by @dsanders2gilead in #103
• add gsm vignette by @kodesiba in #130
• Update Github actions by @jwildfire in #119
• Fix 121 ungroup df input by @mattroumaya in #126
• Fix 123 migrate by @dsanders2gilead in #127
• Fix 106 ie map raw by @dsanders2gilead in #132
• Fix 117 pd map raw by @dsanders2gilead in #128
• PD_Assess at QC level - unit tests, docs, example by @dsanders2gilead in #129
• Workflow updates by @jwildfire in #138
• update check action. fix #146. fix #133. by @jwildfire in #147
• Fix 135 consent map raw by @dsanders2gilead in #141
• testing + docs + example for Consent_Assess, docs could use more expl… by @dsanders2gilead in #143
• Feature disp map by @mattroumaya in #134
• Update to use new RDSL data by @jwildfire in #152
• Refactor Analyze Wilcoxon by @jwildfire in #160
• AE_Assess() qualification by @mattroumaya in #131
• Fix 154 155 qc ie consent analyze by @dsanders2gilead in #156
• Fix 162 transform event count by @dsanders2gilead in #173
• closes #166; update qualification test cases for NAs in AE_Assess() by @mattroumaya in #180
• Create Analyze_Fisher function by @gwu05 in #178
• Flipped the Fisher.Test estimate so ratio is Site of Interest vs Other Sites by @gwu05 in #186
• Rename variables for analyze functions (close #187) by @mattroumaya in #192
• Use clindata v0.3 by @jwildfire in #191
• Release v0.1.0 by @mattroumaya in #194

New Contributors

• @dsanders2gilead made their first contribution in #31
• @gwu05 made their first contribution in #45
• @kodesiba made their first contribution in #109

Full Changelog: https://github.com/Gilead-BioStats/gsm/commits/v0.1.0