Merge pull request #516 from OHDSI/issue-445

Add three new temporal checks: `plausibleAfterBirth`, `plausibleBeforeDeath`, `plausibleStartBeforeEnd`

Author: katy-sadowski

.gitignore

@@ -28,14 +28,16 @@ inst/results.json
 # Other
 .DS_Store
 
+# Visual Studio Code
+.vscode/
+
 errorReport.txt
 output/
 results/
 thresholds/
 hs_err_pid*.log
 docs/Gemfile
 docs/Gemfile.lock
-sql
 vignettes/*.log
 /doc/
 /Meta/

R/executeDqChecks.R

@@ -123,6 +123,7 @@ executeDqChecks <- function(connectionDetails,
     }
   }
 
+
   # temporary patch to work around vroom 1.6.4 bug
   readr::local_edition(1)
 
@@ -258,6 +259,14 @@ executeDqChecks <- function(connectionDetails,
     stop("No checks are available based on excluded tables. Please review tablesToExclude.")
   }
 
+  if ("plausibleDuringLife" %in% checkDescriptionsDf$checkName) {
+    warning("DEPRECATION WARNING - The plausibleDuringLife check has been reimplemented with the plausibleBeforeDeath check.")
+  }
+
+  if ("plausibleTemporalAfter" %in% checkDescriptionsDf$checkName) {
+    warning("DEPRECATION WARNING - The plausibleTemporalAfter check has been reimplemented with the plausibleAfterBirth and plausibleStartBeforeEnd checks.")
+  }
+
   checkDescriptions <- split(checkDescriptionsDf, seq_len(nrow(checkDescriptionsDf)))
 
   connection <- NULL

inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv

@@ -20,5 +20,8 @@ FIELD,plausibleValueHigh,The number and percent of records with a value in the @
 FIELD,plausibleTemporalAfter,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs prior to the date in the @plausibleTemporalAfterFieldName field of the @plausibleTemporalAfterTableName table.,Verification,Plausibility,Temporal,field_plausible_temporal_after.sql,plausibleTemporalAfter=='Yes'
 FIELD,plausibleDuringLife,"If yes, the number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_during_life.sql,plausibleDuringLife=='Yes'
 FIELD,withinVisitDates,The number and percent of records not within one week on either side of the corresponding visit occurrence start and end date,Verification,Conformance,,field_within_visit_dates.sql,withinVisitDates=='Yes'
+FIELD,plausibleAfterBirth,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs prior to birth.",Verification,Plausibility,Temporal,field_plausible_after_birth.sql,plausibleAfterBirth=='Yes'
+FIELD,plausibleBeforeDeath,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_before_death.sql,plausibleBeforeDeath=='Yes'
+FIELD,plausibleStartBeforeEnd,"The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs after the date in the @plausibleStartBeforeEndFieldName.",Verification,Plausibility,Temporal,field_plausible_start_before_end.sql,plausibleStartBeforeEnd=='Yes'
 CONCEPT,plausibleGender,"For a CONCEPT_ID @conceptId (@conceptName), the number and percent of records associated with patients with an implausible gender (correct gender = @plausibleGender).",Validation,Plausibility,Atemporal,concept_plausible_gender.sql,plausibleGender!=''
 CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN  (@plausibleUnitConceptIds)).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!=''

inst/csv/OMOP_CDMv5.2_Field_Level.csv

@@ -20,5 +20,8 @@ FIELD,plausibleValueHigh,The number and percent of records with a value in the @
 FIELD,plausibleTemporalAfter,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs prior to the date in the @plausibleTemporalAfterFieldName field of the @plausibleTemporalAfterTableName table.,Verification,Plausibility,Temporal,field_plausible_temporal_after.sql,plausibleTemporalAfter=='Yes'
 FIELD,plausibleDuringLife,"If yes, the number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_during_life.sql,plausibleDuringLife=='Yes'
 FIELD,withinVisitDates,The number and percent of records not within one week on either side of the corresponding visit occurrence start and end date,Verification,Conformance,,field_within_visit_dates.sql,withinVisitDates=='Yes'
+FIELD,plausibleAfterBirth,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs prior to birth.",Verification,Plausibility,Temporal,field_plausible_after_birth.sql,plausibleAfterBirth=='Yes'
+FIELD,plausibleBeforeDeath,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_before_death.sql,plausibleBeforeDeath=='Yes'
+FIELD,plausibleStartBeforeEnd,"The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs after the date in the @plausibleStartBeforeEndFieldName.",Verification,Plausibility,Temporal,field_plausible_start_before_end.sql,plausibleStartBeforeEnd=='Yes'
 CONCEPT,plausibleGender,"For a CONCEPT_ID @conceptId (@conceptName), the number and percent of records associated with patients with an implausible gender (correct gender = @plausibleGender).",Validation,Plausibility,Atemporal,concept_plausible_gender.sql,plausibleGender!=''
 CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN  (@plausibleUnitConceptIds)).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!=''