sdtmchecks 1.0.0 “CRAN Try”
Refinements of
existing data check functions
Misc package updates
- General updates for CRAN compliance, e.g. to DESCRIPTION file,
Roxygen headers, etc.
- Remove
rm(list=ls()) from sdtmchecksmeta.R (#375)
- Removed
xls2list() function. If working with the
results of run_all_checks() it’s recommended to output
results to to .rds instead of parsing .xlsx files.
sdtmchecks 0.1.11.9008 “Light
Ice”
Refinements of
existing data check functions
check_ae_aeacn_ds_disctx_covid
add more header and unit tests, update header description that the check
specifically looks for DSDECOD = ‘ADVERSE EVENT’ and include a note that
a single DSDECOD = ‘ADVERSE EVENT’ will yield a pass but there may be
multiple records in DS expected with this value #330check_ae_aeacnoth
add more header and unit tests for NA, minor update to return message #328check_ae_aeout
fix logic for the scenario when AEOUT is not populated but there is a
non-missing AEDTHDTC, update return message (#318)check_ae_aesdth_aedthdtc
include AETERM for easier querying, added more header examples, updated
return message. (#323).
Update associated unit test to include AETERM (#324).check_ae_aesdthdtc_aesdth
bug fix for NA values not detected via original
!(AE[["AESDTH"]]=="Y") logic leading to possible false
negative result #247,
include AETERM for easier querying, added more header examples, updated
return message. (#322).
Update associated unit test to include AETERM (#324).check_dd_ae_aeout_aedthdtc
fix logic for the scenario when AEOUT is not populated but there is a
non-missing AEDTHDTC, update return message. This check overlaps with check_ae_aeout,
but both will be retained for now to avoid breaking changes (#310)
Misc package updates
- Update GitHub workflows (#316)
sdtmchecks 0.1.11 “Light Ice”
- Re-create sdtmchecksmeta.RData with MedDRA dictionary version 27.0
listed instead of 26.1 (#312)
Misc package updates
- Unit test accompanying new CE check
check_ce_missing_month()
previously created by @rymarinelli added into
tests/testthat subdirectory
- Fix minor typo in README (#299)
- Add cran-comments.md (#305)
sdtmchecks 0.1.10 “Light Ice”
Refinements of
existing data check functions
New data check functions
check_ce_missing_month()
- flags if CE has a suspicious date value with year and day known but
month missing (#148),
with thanks to @rymarinellicheck_ae_aeout_aeendtc_nonfatal()
- flags AEs with inconsistent AE outcome (AEOUT) and AE resolution date
(AEENDTC) for non-fatal AEs (based on AEOUT) (#113),
with thanks to @J-Lox
Refinements of
existing report utilities
Misc package updates
- Specify version >= 1.1.1 for dplyr version in DESCRIPTION
- Replace “report_diff” with “Status” in
globals.R to
align with update in diff_reports()
(#269)
sdtmchecks 0.1.9 “Bubble and
Squeak”
New report utility functions
- Added
diff_reports()
reporting function to utils.R to compare report objects
generated from run_all_checks(),
enabling identification of records newly flagged (#264),
with thanks to @harriscw
- Include “report_diff” in
globals.R (#265)
Misc package updates
- Automated security update in workflow (#268)
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)
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
New functions
- Added
xls2list()
reporting function to create a list from spreadsheet tabs using the
{openxlsx} package (#85)
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:
- 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:
- 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
Refinements of
existing data check functions
- Updated existing data checks to list the
n function
from {dplyr} in the header (#67):
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
utils.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
Misc updates
- Add CI/CD workflow (#2, #8)
- Add package nickname as
nickname.RData
and reference in data.R, globals.R
- 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:
- 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)