Changelog

Source: NEWS.md

sdtmchecks 0.1.8 “Bubble and Squeak”

Refinements of existing data check functions

• check_tu_rs_new_lesions updated to include overall response of PMD as an indicator of progressive disease. Visit info also added to check result. (#197)
• check_ae_fatal updated to address bug that was causing warning. Logic was subsequently streamlined. (#215)
• Checks that expect specific preferred terms identifying Covid-19 related AEs were updated to warn if that metadata was not provided. (#220 & #223)
• --SEQ variables were removed from checks. (#246)

Metadata updates

• sdtmchecksmeta.RData with descriptive update related to Progressive Metabolic Disease (“PMD”) inclusion in check_tu_rs_new_lesions (#197)

Documentation updates

• Roxygen2 header updated to include @family and @keyword for data check function categories OPHTH and COVID (#214) - applied to the following data checks:
  • COVID:
    • check_ae_aeacn_ds_disctx_covid.R
    • check_ae_aeacnoth_ds_stddisc_covid.R
    • check_dv_ae_aedecod_covid.R
    • check_dv_covid.R
  • OPHTH:
    • check_ae_aelat.R
    • check_cm_cmlat.R
    • check_cm_cmlat_prior_ocular.R
    • check_oe_bcva_1m_late_early_tot.R
    • check_oe_bcva_4m_late_early_tot.R
    • check_oe_bcva_4m_vs_1m_req.R
    • check_oe_bcva_tot_mismatch.R
    • check_oe_sc_lat_count_fingers.R
    • check_pr_prlat.R
    • check_sc_dm_eligcrit.R
    • check_sc_dm_seyeselc.R

sdtmchecks 0.1.6 “Bubble and Squeak”

Refinements of existing data check functions

• Minor update to return message for check_tu_rs_new_lesions() and more header examples added (#98)
• Typo in return message corrected for check_ae_aetoxgr() (#187)

New functions

• Added xls2list() reporting function to create a list from spreadsheet tabs using the {openxlsx} package (#85)

Metadata updates

• sdtmchecksmeta.RData saves as version=2 not version=3 for backwards compatibility with R < 3.5.0 when .RData loaded (#84)

Documentation updates

• New vignettes:
  • Search Data Check Functions published as article on pkgdown site to allow users to search data check functions (check_xx....R) (#71)
  • FAQs page (#130)
• Other minor updates:
  • Edited @title of check_ae_aeacn_ds_disctx_covid(), check_ae_aeacnoth_ds_stddisc_covid() to be single line to address warning during package build
  • Edited headers of dtc_dupl_early() and fail() in utils.R
  • Commented out template assigned in _pkgdown.yml file (#104)
  • Added clickable version releases as links in News dropdown of pkgdown site (#121)
  • Edited headings in Get started article (#114)
  • Added a few bullet points to Writing a New Check
  • Updated pkgdown site based on latest version of {Roxygen2} (v7.2.3) instead of (v7.1.1). DESCRIPTION reflects version in RoxygenNote, and associated man/*.Rd files updated.
  • Roxygen2 header updates to include @family and @keyword for functions in run_all_checks.R, run_check.R, utils.R (#85)
  • Moved sdtmchecks package information from utils.R to sdtmchecks-package.R (#85)

Misc package updates

• Unit tests:
  • Added unit testing (copied in from earlier internal Roche package version) (#126, #112)
  • Included more unit tests to expand coverage (#141), with thanks to @harriscw (#137, #144, #145, #155, #162), @J-Lox (#147, #156), @laywang142 (#199, #158, #153, #146), @sarabodach (#150, #151, #159, #160, #183)
  • Added GitHub action for test coverage report produced by {covr} and uploaded to codecov (#163)
• README:
  • Include badges on README:
    • Test coverage badge from {covr} (#122, #133)
    • R CMD Check badge (#132)
    • CRAN status badge (#132)
  • README.Rmd added to render README.md (#172)
  • Add installation instructions from “https://pharmaverse.r-universe.dev” (devel branch, default) #195, #226
  • Specify recommended installation from main branch: devtools::install_github("pharmaverse/sdtmchecks", ref = "main")
• Updated DESCRIPTION to specify:
  • New dependency: {testthat}
  • GitHub as Repository for sdtmchecks (#123)
  • Config/testthat/edition: 3 (#138)
• Implemented {renv} for package dependency management, adding renvignore, renv.lock, renv subfolder and including updated .Rprofile (#111)
• Package version 0.1.5.1 used prior to update to 0.1.6

sdtmchecks 0.1.5 “Hunter Pi”

New data check functions

• check_ds_multdeath_dsstdtc() - flags if DS has multiple non-missing death dates in DSSTDTC that do not match (#62)

Refinements of existing data check functions

• Updated existing data checks to list the n function from {dplyr} in the header (#67):
  • check_dm_usubjid_dup()
  • check_qs_dup()

Metadata updates

• Metadata corresponding to new data check added to sdtmchecksmeta.RData (#63)
• Update sdtmchecksmeta.RData to reference MedDRA v26.0 instead of v25.1 (#89)

Misc updates

• Clarification added to “Writing a New Check” Vignette if contributor does not have write access to the repo (#65)

sdtmchecks 0.1.4 “Very Cool Nickname”

Refinements of existing data check functions

• Updated existing data checks
  • check_lb_lbstresu() - add more text strings (NEGATIVE, POSITIVE, NOT DONE) allowed for LBORRES to reduce false positives (#27)
  • check_tr_trstresn_ldiam() - include a return message that summarizes total TR records that are missing, NOT DONE, NOT EVALUABLE to help with interpreting the output (#27)
  • check_ae_aeacnoth_ds_disctx() - corrected typo in return message (#56)

New functions

• New helper function utilities added to util.R
  • create_R_script() can use sdtmchecksmeta.RData as input to programmatically generate an R script with function calls (#22)
  • report_to_xlsx() to generate the output results from selected data check functions as an .xlsx file including a tab for each check with potential discrepancies flagged and a summary page with conditional formatting to provide an overview of the results (#11)

New documentation

• “Writing a New Check” published as Vignette (#5)

Misc updates

• Add CI/CD workflow (#2, #8)
• Add package nickname as nickname.RData and reference in data.R, globals.R (#12)
• Remove repeated occurrence of convert_var_to_ascii() from utils.R (#31)

sdtmchecks 0.1.2 “The one without the nickname”

Misc updates

• Removed package nickname from Description

sdtmchecks 0.1.1 “Open Up”

Initial package deployment

• Initial deployment of open-source sdtmchecks Pharmaverse package, based on code migrated from the internal Roche sdtmchecks package, which includes a variety of data checks and utility functions
• All data check functions (check_xx....R) modified from Roche-specific version to include:
  • Updated roxygen2 headers with generalized examples
  • Pre-processing in the function call (preproc=identity,...) to allow company-specific pre-processing
• Proprietary dataset call-ins removed
• Metadata corresponding to all data check functions sdtmchecksmeta.RData added to the data subdirectory; Roche-specific acronyms removed from descriptive text
• Utility functions added within separate roche_utils.R file for Roche-specific processing and to serve as a reference for implementation of company-specific pre-processing
• globals.R added with explicit list to pass through utils::globalVariables()
• Other general utility functions that are invoked within check_xx....R functions consolidated from separate .R scripts into utils.R:
  • pass()
  • fail()
  • is_sas_na()
  • truncate_var_strings()
  • dtc_dupl_early()
  • impute_day01()
  • convert_var_to_ascii()
  • %lacks_all%(), %lacks_any%(), lacks_msg(), %has_all%(), and %has_any%() (from lacks_has.R)
• README, LICENSE, DESCRIPTION, _pkgdown.yml, vignette files tailored to github.com/pharmaverse (#1)
• Package logo added to man/figures
• Package site created via pkgdown

New data check functions (post-migration)

• check_ae_aeacnoth_ds_disctx() flags if an AE record indicates person discontinued from study but there is no corresponding DS record indicating study discontinuation (where DS.DSSCAT = "STUDY COMPLETION/EARLY DISCONTINUATION" and DS.DSDECOD != "COMPLETED") (#3)