check_ae_aeacn_ds_disctx_covid, check_ae_aeacnoth_ds_stddisc_covid, check_dv_ae_aedecod_covid are affected.check_vs_height minor update to return message #379check_lb_missing_month and check_mh_missing_month were both updated to have flexibility for Roche functions parsing --SPIDrm(list=ls()) from sdtmchecksmeta.R (#375)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.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)check_ce_missing_month() previously created by @rymarinelli added into tests/testthat subdirectorycheck_ae_aedthdtc_ds_death updated logic, as this check is primarily useful for legacy studies that mapped DSTERM to have the specific string "DEATH DUE TO ADVERSE EVENT." Newer studies have updated mapping for DSTERM, where the specific AE is concatenated with the string "DEATH DUE TO" - e.g., "DEATH DUE TO INFLUENZA." The check will be based on DEATH DUE TO ADVERSE EVENT given in DSTERM. Studies without this string will be given a pass. (#101).check_ae_aerel updated syntax with more dynamic inclusion of AEREL variables (#259), with thanks to @vrakinavcheck_ss_ssdtc_dead_ds updated to include pre-processing input and return RAVE column if applicable (#263)check_rs_rsdtc_across_visit, check_tr_trdtc_across_visit, check_tu_tudtc_across_visit updated to have more info, e.g., --TESTCD/RAVE info (#260).check_tr_dup with required variables updated and removal of superceded function dplyr::arrange_at() (#271)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-Loxreport_to_xlsx with added PARAM of extrastring=""sdtmchecksmeta.RData with added preproc=roche_derive_rave_row, newly added check_ce_missing_month and check_ae_aeout_aeendtc_nonfatal functions, updated notes for changed logic of check_ae_aedthdtc_ds_deathglobals.R to align with update in diff_reports() (#269)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 @harriscwglobals.R (#265)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)--SEQ variables were removed from checks. (#246)sdtmchecksmeta.RData with descriptive update related to Progressive Metabolic Disease ("PMD") inclusion in check_tu_rs_new_lesions (#197)@family and @keyword for data check function categories OPHTH and COVID (#214) - applied to the following data checks:
check_tu_rs_new_lesions() and more header examples added (#98)check_ae_aetoxgr() (#187)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)New vignettes:
check_xx....R) (#71)Other minor updates:
@title of check_ae_aeacn_ds_disctx_covid(), check_ae_aeacnoth_ds_stddisc_covid() to be single line to address warning during package builddtc_dupl_early() and fail() in utils.RRoxygenNote, and associated man/*.Rd files updated.@family and @keyword for functions in run_all_checks.R, run_check.R, utils.R (#85)utils.R to sdtmchecks-package.R (#85)@harriscw (#137, #144, #145, #155, #162), @J-Lox (#147, #156), @laywang142 (#199, #158, #153, #146), @sarabodach (#150, #151, #159, #160, #183)check_ds_multdeath_dsstdtc() - flags if DS has multiple non-missing death dates in DSSTDTC that do not match (#62)n function from {dplyr} in the header (#67):
sdtmchecksmeta.RData (#63)sdtmchecksmeta.RData to reference MedDRA v26.0 instead of v25.1 (#89)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)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)nickname.RData and reference in data.R, globals.Rconvert_var_to_ascii() from utils.R (#31)check_xx....R) modified from Roche-specific version to include:
preproc=identity,...) to allow company-specific pre-processingsdtmchecksmeta.RData added to the data subdirectory; Roche-specific acronyms removed from descriptive textroche_utils.R file for Roche-specific processing and to serve as a reference for implementation of company-specific pre-processingglobals.R added with explicit list to pass through utils::globalVariables()check_xx....R functions consolidated from separate .R scripts into utils.R:
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)