Function reference • sdtmchecks

Data checks Functions for data checks.
`check_ae_aeacn_ds_disctx_covid()`	Check for COVID-19 AE with DRUG WITHDRAWN action without DS Trt Discon
`check_ae_aeacnoth()`	Check for null AEACNOT1/2 when AEACNOTH = 'MULTIPLE'
`check_ae_aeacnoth_ds_disctx()`	Check if, whenever a patient experiences an AE leading to study discontinuation, they also have a DS record indicating this.
`check_ae_aeacnoth_ds_stddisc_covid()`	Check for COVID-19 AE leading to Study Discon without DS Study Discon
`check_ae_aedecod()`	Check for missing AEDECOD values
`check_ae_aedthdtc_aesdth()`	Check AEs with AEDTHDTC value but AESDTH not "Y"
`check_ae_aedthdtc_ds_death()`	Check for missing AEDTHDTC where DS indicates death due to AE
`check_ae_aelat()`	Check if AESOC has Eye, and Affected Eye is missing
`check_ae_aeout()`	Check for inconsistency between AE outcome (AEOUT) and death date (AEDTHDTC)
`check_ae_aeout_aeendtc_aedthdtc()`	Check for AE outcome (AEOUT) of 'FATAL' with non-missing resolution date that is not equal to the death date
`check_ae_aeout_aeendtc_nonfatal()`	Check for non-fatal AEs with inconsistent AEOUT and AEENDTC
`check_ae_aerel()`	Check for AEREL1 - AERELN when AEREL is missing and when AEREL is unexpected
`check_ae_aesdth_aedthdtc()`	Check AEs with AESDTH of "Y" but No AEDTHDTC Value
`check_ae_aestdtc_after_aeendtc()`	Check that all AE start dates are on or before AE end dates
`check_ae_aestdtc_after_dd()`	Check for AE dates occurring after death date
`check_ae_aetoxgr()`	Check for missing AETOXGR and/or AESEV values
`check_ae_death()`	Check for Grade 5 AE death variable consistency
`check_ae_death_ds_discon()`	Check if death in AE then there should be a study discon form
`check_ae_ds_partial_death_dates()`	Check for partial death dates in AE and DS
`check_ae_dup()`	Check for duplicate AE entries
`check_ae_fatal()`	Check for death variable consistency when AEOUT=="FATAL"
`check_ae_withdr_ds_discon()`	Check if an AE leading to drug being withdrawn is reflected in DS
`check_ce_missing_month()`	Check for clinical events dates with year and day known but month unknown
`check_cm_cmdecod()`	Check for missing CMDECOD values
`check_cm_cmindc()`	Check for concomitant medication indication with text string "PROPHYL" when not given for prophylaxis
`check_cm_cmlat()`	Check if ocular concomitant medication has laterality missing or laterality field is populated but route is not eye-related.
`check_cm_cmlat_prior_ocular()`	Check if ocular concomitant medication has laterality missing for specific "PRIOR OCULAR THERAPIES AND TREATMENTS" (or similar names) CRF page.
`check_cm_missing_month()`	Check for conmed dates with year and day known but month unknown
`check_dd_ae_aedthdtc_ds_dsstdtc()`	Check if death date is the same in AE and DS domains
`check_dd_ae_aeout_aedthdtc()`	Check if there is a death date and AEOUT='FATAL' agreement
`check_dd_death_date()`	Check if patient with Death due to AE also has Death record in DS
`check_dm_actarm_arm()`	Check DM where ARM is not equal to ACTARM
`check_dm_ae_ds_death()`	Check if death reported in DM then death indicator also present in DS or AE
`check_dm_age_missing()`	Check for patients with suspicious age values
`check_dm_armcd()`	Check for missing ARM or ARMCD values in DM
`check_dm_dthfl_dthdtc()`	Check that when DM.DTHFL is Y, DM.DTHDTC does not have a missing value, and vice versa
`check_dm_usubjid_ae_usubjid()`	Check patients in the DM dataset who do not have records in the AE dataset
`check_dm_usubjid_dup()`	Check duplicate patient records in DM based on USUBJID
`check_ds_ae_discon()`	Check for treatment discontinuation consistency between DS and AE
`check_ds_dsdecod_death()`	Check for study discontinuation record if death indicated
`check_ds_dsdecod_dsstdtc()`	Check DS with death record but no death date
`check_ds_dsscat()`	Check for patients with more than one study discontinuation records
`check_ds_dsterm_death_due_to()`	Check missing cause of death information in DS
`check_ds_duplicate_randomization()`	Check for duplicate randomization records for a patient
`check_ds_ex_after_discon()`	Check for patients who had Start/End date of treatment after study discontinuation date
`check_ds_multdeath_dsstdtc()`	Check DS with multiple death records with death dates, where death dates do not match
`check_ds_sc_strat()`	Check if randomized patients are missing stratification factor data
`check_dv_ae_aedecod_covid()`	Check for consistency between DV and AE for COVID-19 events
`check_dv_covid()`	Check for consistency in COVID-19 DV variables, DVREAS and DVEPRELI
`check_ec_sc_lat()`	Check if Study Drug is not administered in the Study Eye
`check_eg_egdtc_visit_ordinal_error()`	Check that all ECG datetimes are earlier than last visit's (possible datetime data entry error)
`check_ex_dup()`	Check for duplicate EX records
`check_ex_exdose_exoccur()`	Check for Missing EXDOSE.
`check_ex_exdose_pos_exoccur_no()`	Check for EXDOSE>0 When EXOCCUR is not "Y"
`check_ex_exdosu()`	Check for missing EXDOSU records
`check_ex_exoccur_exdose_exstdtc()`	Check for Invalid EXDOSE (Dose per Administration) and Missing/Incomplete EXSTDTC (Start Date) Values for valid exposures
`check_ex_exoccur_mis_exdose_nonmis()`	Check for missing EXOCCUR but EXDOSE not missing
`check_ex_exstdtc_after_dd()`	Check for EX dates occurring after death date
`check_ex_exstdtc_after_exendtc()`	Check that all exposure start dates are on or before exposure end dates
`check_ex_exstdtc_visit_ordinal_error()`	Check that all EX start dates are earlier than last visit's (possible datetime data entry error)
`check_ex_extrt_exoccur()`	Check for EX records where EXTRT is missing
`check_ex_infusion_exstdtc_exendtc()`	Check that an infusion drug has same start/end exposure dates, also including missing start/end dates
`check_ex_visit()`	Check for missing EX.VISIT
`check_lb_lbdtc_after_dd()`	Check for LB dates occurring after death date
`check_lb_lbdtc_visit_ordinal_error()`	Check that all LB dates are duplicated or earlier than last visit's (possible datetime data entry error)
`check_lb_lbstnrlo_lbstnrhi()`	Check for missing lab reference ranges (LBSTNRLO, LBSTNRHI)
`check_lb_lbstresc_char()`	Check LBORRES/LBSTRESC populated with number beginning with character '>' or '<', which will yield missing AVAL in ADaM and records will be omitted in analyses such as Hy's Law
`check_lb_lbstresn_missing()`	Check missing standard lab values (LBSTRESN/LBSTRESC)
`check_lb_lbstresu()`	Check for missing lab units (LBSTRESU)
`check_lb_missing_month()`	Check for lab dates with year and day known but month unknown
`check_mh_missing_month()`	Check for MH dates with year and day known but month unknown
`check_mi_mispec()`	Check for missing values in the MISPEC variable
`check_oe_bcva_1m_late_early_tot()`	Check if 1m BCVA test stops too late, too early and has correct total
`check_oe_bcva_4m_late_early_tot()`	Check if 4m BCVA test stops too late, too early and has correct total
`check_oe_bcva_4m_vs_1m_req()`	Check if 1m BCVA test is completed per BCVA 4m result
`check_oe_bcva_tot_mismatch()`	Check mismatch between Derived BCVA Total Score & Total BCVA Score from Data
`check_oe_sc_lat_count_fingers()`	Check if Post Treatment Count Fingers in Study Eye laterality does not match with Subject Characteristics Study Eye laterality
`check_pr_missing_month()`	Check for procedure dates with year and day known but month unknown
`check_pr_prlat()`	Check if ocular procedures/surgeries has laterality missing for CRF pages which contain the word "OCULAR" (and not "NON-OCULAR").
`check_qs_dup()`	Check for multiple dates at the same visit in QS
`check_qs_qsdtc_after_dd()`	Check for QS dates occurring after death date
`check_qs_qsdtc_visit_ordinal_error()`	Check that all QS dates are duplicated or earlier than last visit's (possible datetime data entry error)
`check_qs_qsstat_qsreasnd()`	Check to confirm that there is a reason for a questionnaire being marked as not done
`check_qs_qsstat_qsstresc()`	Check for non-missing QSSTRESC if QSSTAT is NOT DONE
`check_rs_rscat_rsscat()`	Check for patients with populated RSSCAT but missing RSCAT.
`check_rs_rsdtc_across_visit()`	Check RS records where the same date occurs across multiple visits
`check_rs_rsdtc_visit()`	Check missing RSDTC and VISIT
`check_rs_rsdtc_visit_ordinal_error()`	Check that all RS dates for INV Overall Response are duplicated or earlier than last visit's (possible date entry error)
`check_sc_dm_eligcrit()`	Check SC Eye Meeting Eligibility Criteria assignments among DM patients
`check_sc_dm_seyeselc()`	Check SC Study Eye Selection assignments among DM patients
`check_ss_ssdtc_alive_dm()`	Check non-missing last ALIVE status date in SS is before than death date in DM
`check_ss_ssdtc_dead_ds()`	Check non-missing DEAD status date in SS and non-missing according DS record with death date where status date is greater or equal to death date
`check_ss_ssdtc_dead_dthdtc()`	Check non-missing DEAD status date in SS and an according DM record with death date where status date is greater or equal to death date
`check_ss_ssstat_ssorres()`	Check for non-missing SSORRES if SSSTAT is NOT DONE
`check_tr_dup()`	Check for duplicate TR records
`check_tr_trdtc_across_visit()`	Check TR Longest Diameter Records where the same date occurs across multiple visits
`check_tr_trdtc_visit_ordinal_error()`	Check that all TR dates by INV are duplicated or earlier than last visit's (possible date entry error)
`check_tr_trstresn_ldiam()`	Check for TR records with missing TRSTRESN for Longest Diameter (LDIAM)
`check_ts_aedict()`	Check for missing MedDRA version in TS
`check_ts_cmdict()`	Check for missing WHODrug version in TS
`check_ts_sstdtc_ds_consent()`	Check for missing SSTDTC (Study Start Date) in TS
`check_tu_rs_new_lesions()`	Check for consistency between new lesions and overall PD response
`check_tu_tudtc()`	Check for missing TUDTC values
`check_tu_tudtc_across_visit()`	Check TU Records where the same date occurs across multiple visits
`check_tu_tudtc_visit_ordinal_error()`	Check that all TU dates are duplicated or earlier than last visit's (possible datetime data entry error)
`check_tu_tuloc_missing()`	Check for missing TULOC values
`check_vs_height()`	Check for missing height values
`check_vs_sbp_lt_dbp()`	Check that DBP is not higher than SBP in VS
`check_vs_vsdtc_after_dd()`	Check for VS dates occurring after death date
Data check utility functions Helper functions for data checks.
`pass()`	Pass object
`fail()`	Fail object
`is_sas_na()`	Check if the elements could be of any SAS missing data variant
`%lacks_all%`	Check if data frame is missing any of the specified variables
`%lacks_any%`	Check if data frame has at least one variable from a set of specified variables
`lacks_msg()`	Check data frame for mandatory variables and specify which are missing in message
`%has_all%`	Check if data frame has all specified variables
`%has_any%`	Check if data frame has at least one of the specified variables
`impute_day01()`	Add day of "01" to dates that are in the format of "yyyy-mm"
`dtc_dupl_early()`	Check if start dates are duplicated or earlier than prior visit date
`missing_month()`	Function to check if month is missing while year and day are non-missing (i.e. would be in the format of "yyyy---dd")
Metadata Datasets used with the package.
`sdtmchecksmeta`	Metadata for sdtmchecks
`nickname`	Nickname for package version
Reporting-related programs Example programs for running one or more data checks
`diff_reports()`	Create a sdtmchecks list object with column indicating whether the issue was previously seen
`report_to_xlsx()`	Save report as an xlsx file
`run_all_checks()`	Run all data checks in sdtmchecks package using parallel processing
`run_check()`	Run a single check in sdtmchecks package
Reporting-related utility functions Samples for using the package.
`convert_var_to_ascii()`	Remove non-ASCII characters from reported term in order for Pandoc to create PDF file
`create_R_script()`	Create .R file with sdtmchecks function calls
`truncate_var_strings()`	Utility function to truncate data in var_name
`xlsx2list()`	Create list from tabs of spreadsheet (*xlsx)
Company-specific utility functions Helper functions for data checks tailored to company-specific data inputs.
`roche_derive_rave_row()`	Utility function to obtain Rave form name and row number
`roche_covid_df()`	Check MedDRA version in TS and return dataframe with covid terms according to this version

Reference

Data checks

Data check utility functions

Metadata

Reporting-related programs

Reporting-related utility functions

Company-specific utility functions