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"check_ae_aedthdtc_ds_death" ] }, { "page": "check_ae_aelat", "title": "Check if AESOC has Eye, and Affected Eye is missing", "concept": [ "OPHTH" ], "topics": [ "check_ae_aelat" ] }, { "page": "check_ae_aeout", "title": "Check for inconsistency between AE outcome (AEOUT) and death date (AEDTHDTC)", "topics": [ "check_ae_aeout" ] }, { "page": "check_ae_aeout_aeendtc_aedthdtc", "title": "Check for AE outcome (AEOUT) of 'FATAL' with non-missing resolution date that is not equal to the death date", "topics": [ "check_ae_aeout_aeendtc_aedthdtc" ] }, { "page": "check_ae_aeout_aeendtc_nonfatal", "title": "Check for non-fatal AEs with inconsistent AEOUT and AEENDTC", "topics": [ "check_ae_aeout_aeendtc_nonfatal" ] }, { "page": "check_ae_aerel", "title": "Check for AEREL1 - AERELN when AEREL is missing and when AEREL is unexpected", "topics": [ "check_ae_aerel" ] }, { "page": "check_ae_aesdth_aedthdtc", "title": "Check AEs with AESDTH of \"Y\" but No AEDTHDTC Value", "topics": [ "check_ae_aesdth_aedthdtc" ] }, { "page": "check_ae_aestdtc_after_aeendtc", "title": "Check that all AE start dates are on or before AE end dates", "topics": [ "check_ae_aestdtc_after_aeendtc" ] }, { "page": "check_ae_aestdtc_after_dd", "title": "Check for AE dates occurring after death date", "topics": [ "check_ae_aestdtc_after_dd" ] }, { "page": "check_ae_aetoxgr", "title": "Check for missing AETOXGR and/or AESEV values", "topics": [ "check_ae_aetoxgr" ] }, { "page": "check_ae_death", "title": "Check for Grade 5 AE death variable consistency", "topics": [ "check_ae_death" ] }, { "page": "check_ae_death_ds_discon", "title": "Check if death in AE then there should be a study discon form", "topics": [ "check_ae_death_ds_discon" ] }, { "page": "check_ae_ds_partial_death_dates", "title": "Check for partial death dates in AE and DS", "topics": [ "check_ae_ds_partial_death_dates" ] }, { "page": "check_ae_dup", "title": "Check for duplicate AE entries", "topics": [ "check_ae_dup" ] }, { "page": "check_ae_fatal", "title": "Check for death variable consistency when AEOUT==\"FATAL\"", "topics": [ "check_ae_fatal" ] }, { "page": "check_ae_withdr_ds_discon", "title": "Check if an AE leading to drug being withdrawn is reflected in DS", "topics": [ "check_ae_withdr_ds_discon" ] }, { "page": "check_ce_missing_month", "title": "Check for clinical events dates with year and day known but month unknown", "topics": [ "check_ce_missing_month" ] }, { "page": "check_cm_cmdecod", "title": "Check for missing CMDECOD values", "topics": [ "check_cm_cmdecod" ] }, { "page": "check_cm_cmindc", "title": "Check for concomitant medication indication with text string \"PROPHYL\" when not given for prophylaxis", "topics": [ "check_cm_cmindc" ] }, { "page": "check_cm_cmlat", "title": "Check if ocular concomitant medication has laterality missing or laterality field is populated but route is not eye-related.", "concept": [ "OPHTH" ], "topics": [ "check_cm_cmlat" ] }, { "page": "check_cm_cmlat_prior_ocular", "title": "Check if ocular concomitant medication has laterality missing for specific \"PRIOR OCULAR THERAPIES AND TREATMENTS\" (or similar names) CRF page.", "concept": [ "OPHTH" ], "topics": [ "check_cm_cmlat_prior_ocular" ] }, { "page": "check_cm_missing_month", "title": "Check for conmed dates with year and day known but month unknown", "topics": [ "check_cm_missing_month" ] }, { "page": "check_dd_ae_aedthdtc_ds_dsstdtc", "title": "Check if death date is the same in AE and DS domains", "topics": [ "check_dd_ae_aedthdtc_ds_dsstdtc" ] }, { "page": "check_dd_ae_aeout_aedthdtc", "title": "Check if there is a death date and AEOUT='FATAL' agreement", "topics": [ "check_dd_ae_aeout_aedthdtc" ] }, { "page": "check_dd_death_date", "title": "Check if patient with Death due to AE also has Death record in DS", "topics": [ "check_dd_death_date" ] }, { "page": "check_dm_actarm_arm", "title": "Check DM where ARM is not equal to ACTARM", "topics": [ "check_dm_actarm_arm" ] }, { "page": "check_dm_ae_ds_death", "title": "Check if death reported in DM then death indicator also present in DS or AE", "topics": [ "check_dm_ae_ds_death" ] }, { "page": "check_dm_age_missing", "title": "Check for patients with suspicious age values", "topics": [ "check_dm_age_missing" ] }, { "page": "check_dm_armcd", "title": "Check for missing ARM or ARMCD values in DM", "topics": [ "check_dm_armcd" ] }, { "page": "check_dm_dthfl_dthdtc", "title": "Check that when DM.DTHFL is Y, DM.DTHDTC does not have a missing value, and vice versa", "topics": [ "check_dm_dthfl_dthdtc" ] }, { "page": "check_dm_usubjid_ae_usubjid", "title": "Check patients in the DM dataset who do not have records in the AE dataset", "topics": [ "check_dm_usubjid_ae_usubjid" ] }, { "page": "check_dm_usubjid_dup", "title": "Check duplicate patient records in DM based on USUBJID", "topics": [ "check_dm_usubjid_dup" ] }, { "page": "check_ds_ae_discon", "title": "Check for treatment discontinuation consistency between DS and AE", "topics": [ "check_ds_ae_discon" ] }, { "page": "check_ds_dsdecod_death", "title": "Check for study discontinuation record if death indicated", "topics": [ "check_ds_dsdecod_death" ] }, { "page": "check_ds_dsdecod_dsstdtc", "title": "Check DS with death record but no death date", "topics": [ "check_ds_dsdecod_dsstdtc" ] }, { "page": "check_ds_dsscat", "title": "Check for patients with more than one study discontinuation records", "topics": [ "check_ds_dsscat" ] }, { "page": "check_ds_dsterm_death_due_to", "title": "Check missing cause of death information in DS", "topics": [ "check_ds_dsterm_death_due_to" ] }, { "page": "check_ds_duplicate_randomization", "title": "Check for duplicate randomization records for a patient", "topics": [ "check_ds_duplicate_randomization" ] }, { "page": "check_ds_ex_after_discon", "title": "Check for patients who had Start/End date of treatment after study discontinuation date", "topics": [ "check_ds_ex_after_discon" ] }, { "page": "check_ds_multdeath_dsstdtc", "title": "Check DS with multiple death records with death dates, where death dates do not match", "topics": [ "check_ds_multdeath_dsstdtc" ] }, { "page": "check_ds_sc_strat", "title": "Check if randomized patients are missing stratification factor data", "topics": [ "check_ds_sc_strat" ] }, { "page": "check_dv_ae_aedecod_covid", "title": "Check for consistency between DV and AE for COVID-19 events", "concept": [ "COVID" ], "topics": [ "check_dv_ae_aedecod_covid" ] }, { "page": "check_dv_covid", "title": "Check for consistency in COVID-19 DV variables, DVREAS and DVEPRELI", "concept": [ "COVID" ], "topics": [ "check_dv_covid" ] }, { "page": "check_ec_sc_lat", "title": "Check if Study Drug is not administered in the Study Eye", "topics": [ "check_ec_sc_lat" ] }, { "page": "check_eg_egdtc_visit_ordinal_error", "title": "Check that all ECG datetimes are earlier than last visit's (possible datetime data entry error)", "topics": [ "check_eg_egdtc_visit_ordinal_error" ] }, { "page": "check_ex_dup", "title": "Check for duplicate EX records", "topics": [ "check_ex_dup" ] }, { "page": "check_ex_exdose_exoccur", "title": "Check for Missing EXDOSE.", "topics": [ "check_ex_exdose_exoccur" ] }, { "page": "check_ex_exdose_pos_exoccur_no", "title": "Check for EXDOSE>0 When EXOCCUR is not \"Y\"", "topics": [ "check_ex_exdose_pos_exoccur_no" ] }, { "page": "check_ex_exdosu", "title": "Check for missing EXDOSU records", "topics": [ "check_ex_exdosu" ] }, { "page": "check_ex_exoccur_exdose_exstdtc", "title": "Check for Invalid EXDOSE (Dose per Administration) and Missing/Incomplete EXSTDTC (Start Date) Values for valid exposures", "topics": [ "check_ex_exoccur_exdose_exstdtc" ] }, { "page": "check_ex_exoccur_mis_exdose_nonmis", "title": "Check for missing EXOCCUR but EXDOSE not missing", "topics": [ "check_ex_exoccur_mis_exdose_nonmis" ] }, { "page": "check_ex_exstdtc_after_dd", "title": "Check for EX dates occurring after death date", "topics": [ "check_ex_exstdtc_after_dd" ] }, { "page": "check_ex_exstdtc_after_exendtc", "title": "Check that all exposure start dates are on or before exposure end dates", "topics": [ "check_ex_exstdtc_after_exendtc" ] }, { "page": "check_ex_exstdtc_visit_ordinal_error", "title": "Check that all EX start dates are earlier than last visit's (possible datetime data entry error)", "topics": [ "check_ex_exstdtc_visit_ordinal_error" ] }, { "page": "check_ex_extrt_exoccur", "title": "Check for EX records where EXTRT is missing", "topics": [ "check_ex_extrt_exoccur" ] }, { "page": "check_ex_infusion_exstdtc_exendtc", "title": "Check that an infusion drug has same start/end exposure dates, also including missing start/end dates", "topics": [ "check_ex_infusion_exstdtc_exendtc" ] }, { "page": "check_ex_visit", "title": "Check for missing EX.VISIT", "topics": [ "check_ex_visit" ] }, { "page": "check_lb_lbdtc_after_dd", "title": "Check for LB dates occurring after death date", "topics": [ "check_lb_lbdtc_after_dd" ] }, { "page": "check_lb_lbdtc_visit_ordinal_error", "title": "Check that all LB dates are duplicated or earlier than last visit's (possible datetime data entry error)", "topics": [ "check_lb_lbdtc_visit_ordinal_error" ] }, { "page": "check_lb_lbstnrlo_lbstnrhi", "title": "Check for missing lab reference ranges (LBSTNRLO, LBSTNRHI)", "topics": [ "check_lb_lbstnrlo_lbstnrhi" ] }, { "page": "check_lb_lbstresc_char", "title": "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", "topics": [ "check_lb_lbstresc_char" ] }, { "page": "check_lb_lbstresn_missing", "title": "Check missing standard lab values (LBSTRESN/LBSTRESC)", "topics": [ "check_lb_lbstresn_missing" ] }, { "page": "check_lb_lbstresu", "title": "Check for missing lab units (LBSTRESU)", "topics": [ "check_lb_lbstresu" ] }, { "page": "check_lb_missing_month", "title": "Check for lab dates with year and day known but month unknown", "topics": [ "check_lb_missing_month" ] }, { "page": "check_mh_missing_month", "title": "Check for MH dates with year and day known but month unknown", "topics": [ "check_mh_missing_month" ] }, { "page": "check_mi_mispec", "title": "Check for missing values in the MISPEC variable", "topics": [ "check_mi_mispec" ] }, { "page": "check_oe_bcva_1m_late_early_tot", "title": "Check if 1m BCVA test stops too late, too early and has correct total", "concept": [ "OPHTH" ], "topics": [ "check_oe_bcva_1m_late_early_tot" ] }, { "page": "check_oe_bcva_4m_late_early_tot", "title": "Check if 4m BCVA test stops too late, too early and has correct total", "concept": [ "OPHTH" ], "topics": [ "check_oe_bcva_4m_late_early_tot" ] }, { "page": "check_oe_bcva_4m_vs_1m_req", "title": "Check if 1m BCVA test is completed per BCVA 4m result", "concept": [ "OPHTH" ], "topics": [ "check_oe_bcva_4m_vs_1m_req" ] }, { "page": "check_oe_bcva_tot_mismatch", "title": "Check mismatch between Derived BCVA Total Score & Total BCVA Score from Data", "concept": [ "OPHTH" ], "topics": [ "check_oe_bcva_tot_mismatch" ] }, { "page": "check_oe_sc_lat_count_fingers", "title": "Check if Post Treatment Count Fingers in Study Eye laterality does not match with Subject Characteristics Study Eye laterality", "concept": [ "OPHTH" ], "topics": [ "check_oe_sc_lat_count_fingers" ] }, { "page": "check_pr_missing_month", "title": "Check for procedure dates with year and day known but month unknown", "topics": [ "check_pr_missing_month" ] }, { "page": "check_pr_prlat", "title": "Check if ocular procedures/surgeries has laterality missing for CRF pages which contain the word \"OCULAR\" (and not \"NON-OCULAR\").", "concept": [ "OPHTH" ], "topics": [ "check_pr_prlat" ] }, { "page": "check_qs_dup", "title": "Check for multiple dates at the same visit in QS", "topics": [ "check_qs_dup" ] }, { "page": "check_qs_qsdtc_after_dd", "title": "Check for QS dates occurring after death date", "topics": [ "check_qs_qsdtc_after_dd" ] }, { "page": "check_qs_qsdtc_visit_ordinal_error", "title": "Check that all QS dates are duplicated or earlier than last visit's (possible datetime data entry error)", "topics": [ "check_qs_qsdtc_visit_ordinal_error" ] }, { "page": "check_qs_qsstat_qsreasnd", "title": "Check to confirm that there is a reason for a questionnaire being marked as not done", "topics": [ "check_qs_qsstat_qsreasnd" ] }, { "page": "check_qs_qsstat_qsstresc", "title": "Check for non-missing QSSTRESC if QSSTAT is NOT DONE", "topics": [ "check_qs_qsstat_qsstresc" ] }, { "page": "check_rs_rscat_rsscat", "title": "Check for patients with populated RSSCAT but missing RSCAT.", "topics": [ "check_rs_rscat_rsscat" ] }, { "page": "check_rs_rsdtc_across_visit", "title": "Check RS records where the same date occurs across multiple visits", "topics": [ "check_rs_rsdtc_across_visit" ] }, { "page": "check_rs_rsdtc_visit", "title": "Check missing RSDTC and VISIT", "topics": [ "check_rs_rsdtc_visit" ] }, { "page": "check_rs_rsdtc_visit_ordinal_error", "title": "Check that all RS dates for INV Overall Response are duplicated or earlier than last visit's (possible date entry error)", "topics": [ "check_rs_rsdtc_visit_ordinal_error" ] }, { "page": "check_sc_dm_eligcrit", "title": "Check SC Eye Meeting Eligibility Criteria assignments among DM patients", "concept": [ "OPHTH" ], "topics": [ "check_sc_dm_eligcrit" ] }, { "page": "check_sc_dm_seyeselc", "title": "Check SC Study Eye Selection assignments among DM patients", "concept": [ "OPHTH" ], "topics": [ "check_sc_dm_seyeselc" ] }, { "page": "check_ss_ssdtc_alive_dm", "title": "Check non-missing last ALIVE status date in SS is before than death date in DM", "topics": [ "check_ss_ssdtc_alive_dm" ] }, { "page": "check_ss_ssdtc_dead_ds", "title": "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", "topics": [ "check_ss_ssdtc_dead_ds" ] }, { "page": "check_ss_ssdtc_dead_dthdtc", "title": "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", "topics": [ "check_ss_ssdtc_dead_dthdtc" ] }, { "page": "check_ss_ssstat_ssorres", "title": "Check for non-missing SSORRES if SSSTAT is NOT DONE", "topics": [ "check_ss_ssstat_ssorres" ] }, { "page": "check_tr_dup", "title": "Check for duplicate TR records", "topics": [ "check_tr_dup" ] }, { "page": "check_tr_trdtc_across_visit", "title": "Check TR Longest Diameter Records where the same date occurs across multiple visits", "topics": [ "check_tr_trdtc_across_visit" ] }, { "page": "check_tr_trdtc_visit_ordinal_error", "title": "Check that all TR dates by INV are duplicated or earlier than last visit's (possible date entry error)", "topics": [ "check_tr_trdtc_visit_ordinal_error" ] }, { "page": "check_tr_trstresn_ldiam", "title": "Check for TR records with missing TRSTRESN for Longest Diameter (LDIAM)", "topics": [ "check_tr_trstresn_ldiam" ] }, { "page": "check_ts_aedict", "title": "Check for missing MedDRA version in TS", "topics": [ "check_ts_aedict" ] }, { "page": "check_ts_cmdict", "title": "Check for missing WHODrug version in TS", "topics": [ "check_ts_cmdict" ] }, { "page": "check_ts_sstdtc_ds_consent", "title": "Check for missing SSTDTC (Study Start Date) in TS", "topics": [ "check_ts_sstdtc_ds_consent" ] }, { "page": "check_tu_rs_new_lesions", "title": "Check for consistency between new lesions and overall PD response", "topics": [ "check_tu_rs_new_lesions" ] }, { "page": "check_tu_tudtc", "title": "Check for missing TUDTC values", "topics": [ "check_tu_tudtc" ] }, { "page": "check_tu_tudtc_across_visit", "title": "Check TU Records where the same date occurs across multiple visits", "topics": [ "check_tu_tudtc_across_visit" ] }, { "page": "check_tu_tudtc_visit_ordinal_error", "title": "Check that all TU dates are duplicated or earlier than last visit's (possible datetime data entry error)", "topics": [ "check_tu_tudtc_visit_ordinal_error" ] }, { "page": "check_tu_tuloc_missing", "title": "Check for missing TULOC values", "topics": [ "check_tu_tuloc_missing" ] }, { "page": "check_vs_height", "title": "Check for missing height values", "topics": [ "check_vs_height" ] }, { "page": "check_vs_sbp_lt_dbp", "title": "Check that DBP is not higher than SBP in VS", "topics": [ "check_vs_sbp_lt_dbp" ] }, { "page": "check_vs_vsdtc_after_dd", "title": "Check for VS dates occurring after death date", "topics": [ "check_vs_vsdtc_after_dd" ] }, { "page": "create_R_script", "title": "Create .R file with sdtmchecks function calls", "concept": [ "utils_rpt" ], "topics": [ "create_R_script" ] }, { "page": "diff_reports", "title": "Create a sdtmchecks list object with column indicating whether the issue was previously seen", "concept": [ "ex_rpt" ], "topics": [ "diff_reports" ] }, { "page": "run_all_checks", "title": "Run all data checks in sdtmchecks package using parallel processing", "concept": [ "ex_rpt" ], "topics": [ "run_all_checks" ] }, { "page": "run_check", "title": "Run a single check in sdtmchecks package", "concept": [ "ex_rpt" ], "topics": [ "run_check" ] }, { "page": "sdtmchecksmeta", "title": "Metadata for sdtmchecks", "topics": [ "sdtmchecksmeta" ] } ], "_readme": "https://github.com/pharmaverse/sdtmchecks/raw/HEAD/README.md", "_rundeps": [ "cli", "dplyr", "generics", "glue", "lifecycle", "magrittr", "openxlsx", "pillar", "pkgconfig", "R6", "Rcpp", "rlang", "stringi", "tibble", "tidyselect", "utf8", "vctrs", "withr", "zip" ], "_vignettes": [ { "source": "faqs.Rmd", "filename": "faqs.html", "title": "Frequently Asked Questions (FAQs)", "engine": "knitr::rmarkdown", "headings": [ "Using the package", "Data checks", "Relationship to other tools and data standards", "Package maintenance and release schedule", "Contributing" ], "created": "2023-06-22 08:11:13", "modified": "2023-12-22 21:44:00", "commits": 3 }, { "source": "sdtmchecks.Rmd", "filename": "sdtmchecks.html", "title": "Introduction to sdtmchecks", "engine": "knitr::rmarkdown", "headings": [ "Setting Up", "Documentation", "Metadata", "Running a Check", "Running Many Checks", "Writing Out Results", "Making a Customizable Script" ], "created": "2022-12-02 20:26:57", "modified": "2023-08-26 00:06:26", "commits": 7 }, { "source": "search_checks.Rmd", "filename": "search_checks.html", "title": "Search Data Check Functions", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-06-16 05:13:00", "modified": "2023-06-16 05:13:00", "commits": 1 }, { "source": "write_a_check.Rmd", "filename": "write_a_check.html", "title": "Writing a New Check", "engine": "knitr::rmarkdown", "headings": [ "Background", "Working Collaboratively", "GitHub", "Package Dependencies", "Existing Checks", "Good Practices", "Example Check", "Additional Considerations" ], "created": "2022-10-26 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