diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R index 889bf388..9fa048f5 100644 --- a/R/executeDqChecks.R +++ b/R/executeDqChecks.R @@ -46,6 +46,7 @@ #' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied. #' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied. #' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied. +#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied. #' #' @return If sqlOnly = FALSE, a list object of results #' @@ -77,7 +78,8 @@ executeDqChecks <- function(connectionDetails, cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", - conceptCheckThresholdLoc = "default") { + conceptCheckThresholdLoc = "default", + systemFileNamespace = "DataQualityDashboard") { # Check input ------------------------------------------------------------------------------------------------------------------- if (!("connectionDetails" %in% class(connectionDetails))){ stop("connectionDetails must be an object of class 'connectionDetails'.") @@ -165,24 +167,25 @@ executeDqChecks <- function(connectionDetails, file = system.file( "csv", sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion), - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE ) tableChecks <- .readThresholdFile( checkThresholdLoc = tableCheckThresholdLoc, - defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion) + defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion), + systemFileNamespace ) fieldChecks <- .readThresholdFile( checkThresholdLoc = fieldCheckThresholdLoc, - defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion) + defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion, systemFileNamespace) ) conceptChecks <- .readThresholdFile( checkThresholdLoc = conceptCheckThresholdLoc, - defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion) + defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion, systemFileNamespace) ) # ensure we use only checks that are intended to be run ----------------------------------------- diff --git a/R/listChecks.R b/R/listChecks.R index 0a295a5f..5f71e1c7 100644 --- a/R/listChecks.R +++ b/R/listChecks.R @@ -25,16 +25,16 @@ #' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied. #' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied. #' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied. -#' +#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied. #' #' @export -listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default",conceptCheckThresholdLoc = "default") { +listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default",conceptCheckThresholdLoc = "default", systemFileNamespace = "DataQualityDashboard") { dqChecks <- {} dqChecks$checkDescriptions <- read.csv(system.file( "csv", sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion), - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE) @@ -45,7 +45,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", system.file( "csv", sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion), - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE, na.strings = c(" ", "") @@ -64,7 +64,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", system.file( "csv", sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion), - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE, na.strings = c(" ", "") @@ -83,7 +83,7 @@ listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", system.file( "csv", sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion), - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE, na.strings = c(" ", "") diff --git a/R/reEvaluateThresholds.R b/R/reEvaluateThresholds.R index f8515d67..ab979a61 100644 --- a/R/reEvaluateThresholds.R +++ b/R/reEvaluateThresholds.R @@ -27,7 +27,8 @@ #' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied. #' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied. #' @param cdmVersion The CDM version to target for the data source. By default, 5.3 is used. -#' +#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied. +#' #' @export reEvaluateThresholds <- function(jsonFilePath, @@ -36,7 +37,8 @@ reEvaluateThresholds <- function(jsonFilePath, tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", conceptCheckThresholdLoc = "default", - cdmVersion = '5.3') { + cdmVersion = '5.3', + systemFileNamespace = "DataQualityDashboard") { # Read in results to data frame -------------------------------------- dqdResults <- jsonlite::read_json(path = jsonFilePath) @@ -47,10 +49,10 @@ reEvaluateThresholds <- function(jsonFilePath, df <- do.call(plyr::rbind.fill, df) # Read in new thresholds ---------------------------------------------- - tableChecks <- .readThresholdFile(tableCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion)) - fieldChecks <- .readThresholdFile(fieldCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion)) + tableChecks <- .readThresholdFile(tableCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion), systemFileNamespace) + fieldChecks <- .readThresholdFile(fieldCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion), systemFileNamespace) fieldChecks$cdmFieldName <- toupper(fieldChecks$cdmFieldName) # Uppercase in results, lowercase in threshold files - conceptChecks <- .readThresholdFile(conceptCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion)) + conceptChecks <- .readThresholdFile(conceptCheckThresholdLoc, defaultLoc = sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion), systemFileNamespace) conceptChecks$cdmFieldName <- toupper(conceptChecks$cdmFieldName) newCheckResults <- .evaluateThresholds(df, tableChecks, fieldChecks, conceptChecks) diff --git a/R/readThresholdFile.R b/R/readThresholdFile.R index 55a053f8..83ffaa2e 100644 --- a/R/readThresholdFile.R +++ b/R/readThresholdFile.R @@ -1,10 +1,10 @@ -.readThresholdFile <- function(checkThresholdLoc, defaultLoc) { +.readThresholdFile <- function(checkThresholdLoc, defaultLoc, systemFileNamespace = "DataQualityDashboard") { if (checkThresholdLoc == "default") { result <- read.csv( file = system.file( "csv", defaultLoc, - package = "DataQualityDashboard" + package = systemFileNamespace ), stringsAsFactors = FALSE, na.strings = c(" ","") diff --git a/R/runCheck.R b/R/runCheck.R index bc70be3e..805d010f 100644 --- a/R/runCheck.R +++ b/R/runCheck.R @@ -50,9 +50,11 @@ setNames(check[c], c) }) + packageName <- if(!is.null(checkDescription$packageName)) checkDescription$packageName else "DataQualityDashboard" + params <- c(list(dbms = connectionDetails$dbms), list(sqlFilename = checkDescription$sqlFile), - list(packageName = "DataQualityDashboard"), + list(packageName = packageName), list(warnOnMissingParameters = FALSE), list(cdmDatabaseSchema = cdmDatabaseSchema), list(cohortDatabaseSchema = cohortDatabaseSchema), diff --git a/extras/execution.R b/extras/execution.R index 821d3556..126e12b6 100644 --- a/extras/execution.R +++ b/extras/execution.R @@ -163,7 +163,8 @@ #' @param tableCheckThresholdLoc The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied. #' @param fieldCheckThresholdLoc The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied. #' @param conceptCheckThresholdLoc The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied. -#' +#' @param systemFileNamespace The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied. +#' #' @return If sqlOnly = FALSE, a list object of results #' #' @importFrom magrittr %>% @@ -192,7 +193,8 @@ executeDqChecks <- function(connectionDetails, cdmVersion = "5.3.1", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", - conceptCheckThresholdLoc = "default") { + conceptCheckThresholdLoc = "default", + systemFileNamespace = "DataQualityDashboard") { # Check input ------------------------------------------------------------------------------------------------------------------- if (!("connectionDetails" %in% class(connectionDetails))){ stop("connectionDetails must be an object of class 'connectionDetails'.") @@ -277,25 +279,25 @@ executeDqChecks <- function(connectionDetails, startTime <- Sys.time() checkDescriptionsDf <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Check_Descriptions.csv", cdmVersion), - package = "DataQualityDashboard"), + package = systemFileNamespace), stringsAsFactors = FALSE) if (tableCheckThresholdLoc == "default"){ tableChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Table_Level.csv", cdmVersion), - package = "DataQualityDashboard"), + package = systemFileNamespace), stringsAsFactors = FALSE, na.strings = c(" ",""))} else {tableChecks <- read.csv(tableCheckThresholdLoc, stringsAsFactors = FALSE, na.strings = c(" ",""))} if (fieldCheckThresholdLoc == "default"){ fieldChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Field_Level.csv", cdmVersion), - package = "DataQualityDashboard"), + package = systemFileNamespace), stringsAsFactors = FALSE, na.strings = c(" ",""))} else {fieldChecks <- read.csv(fieldCheckThresholdLoc, stringsAsFactors = FALSE, na.strings = c(" ",""))} if (conceptCheckThresholdLoc == "default"){ conceptChecks <- read.csv(system.file("csv", sprintf("OMOP_CDMv%s_Concept_Level.csv", cdmVersion), - package = "DataQualityDashboard"), + package = systemFileNamespace), stringsAsFactors = FALSE, na.strings = c(" ",""))} else {conceptChecks <- read.csv(conceptCheckThresholdLoc, stringsAsFactors = FALSE, na.strings = c(" ",""))} diff --git a/inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv b/inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv index 22630353..c64f2c97 100644 --- a/inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv +++ b/inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv @@ -1,24 +1,24 @@ -checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,evaluationFilter -TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification. ,Verification,Conformance,Relational,table_cdm_table.sql,cdmTableName!='' -TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,measurePersonCompleteness=='Yes' +checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,packageName,evaluationFilter +TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification.,Verification,Conformance,Relational,table_cdm_table.sql,DataQualityDashboard,cdmTableName!='' +TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,DataQualityDashboard,measurePersonCompleteness=='Yes' TABLE,measureConditionEraCompleteness,"The number and Percent of persons that does not have condition_era built successfully -for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,measureConditionEraCompleteness=='Yes' -FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification. ,Verification,Conformance,Relational,field_cdm_field.sql,cdmFieldName!='' -FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,isRequired=='Yes' -FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,cdmDatatype=='integer' -FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,isPrimaryKey=='Yes' -FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,isForeignKey=='Yes' -FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,isForeignKey=='Yes' & fkDomain!= '' -FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,isForeignKey=='Yes' & fkClass!='' -FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table. ",Verification,Conformance,Value,field_is_standard_valid_concept.sql,isStandardValidConcept=='Yes' -FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,measureValueCompleteness=='Yes' -FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,standardConceptRecordCompleteness=='Yes' -FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,sourceConceptRecordCompleteness=='Yes' -FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,sourceValueCompleteness=='Yes' -FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,plausibleValueLow!='' -FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,plausibleValueHigh!='' -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' -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!='' \ No newline at end of file +for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,DataQualityDashboard,measureConditionEraCompleteness=='Yes' +FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification.,Verification,Conformance,Relational,field_cdm_field.sql,DataQualityDashboard,cdmFieldName!='' +FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,DataQualityDashboard,isRequired=='Yes' +FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,DataQualityDashboard,cdmDatatype=='integer' +FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,DataQualityDashboard,isPrimaryKey=='Yes' +FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,DataQualityDashboard,isForeignKey=='Yes' +FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,DataQualityDashboard,isForeignKey=='Yes' & fkDomain!= '' +FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,DataQualityDashboard,isForeignKey=='Yes' & fkClass!='' +FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table.",Verification,Conformance,Value,field_is_standard_valid_concept.sql,DataQualityDashboard,isStandardValidConcept=='Yes' +FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,DataQualityDashboard,measureValueCompleteness=='Yes' +FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,standardConceptRecordCompleteness=='Yes' +FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,sourceConceptRecordCompleteness=='Yes' +FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,DataQualityDashboard,sourceValueCompleteness=='Yes' +FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,DataQualityDashboard,plausibleValueLow!='' +FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,DataQualityDashboard,plausibleValueHigh!='' +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,DataQualityDashboard,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,DataQualityDashboard,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,DataQualityDashboard,withinVisitDates=='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,DataQualityDashboard,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,DataQualityDashboard,plausibleUnitConceptIdsThreshold!='' diff --git a/inst/csv/OMOP_CDMv5.3_Check_Descriptions.csv b/inst/csv/OMOP_CDMv5.3_Check_Descriptions.csv index 22630353..c64f2c97 100644 --- a/inst/csv/OMOP_CDMv5.3_Check_Descriptions.csv +++ b/inst/csv/OMOP_CDMv5.3_Check_Descriptions.csv @@ -1,24 +1,24 @@ -checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,evaluationFilter -TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification. ,Verification,Conformance,Relational,table_cdm_table.sql,cdmTableName!='' -TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,measurePersonCompleteness=='Yes' +checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,packageName,evaluationFilter +TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification.,Verification,Conformance,Relational,table_cdm_table.sql,DataQualityDashboard,cdmTableName!='' +TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,DataQualityDashboard,measurePersonCompleteness=='Yes' TABLE,measureConditionEraCompleteness,"The number and Percent of persons that does not have condition_era built successfully -for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,measureConditionEraCompleteness=='Yes' -FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification. ,Verification,Conformance,Relational,field_cdm_field.sql,cdmFieldName!='' -FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,isRequired=='Yes' -FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,cdmDatatype=='integer' -FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,isPrimaryKey=='Yes' -FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,isForeignKey=='Yes' -FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,isForeignKey=='Yes' & fkDomain!= '' -FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,isForeignKey=='Yes' & fkClass!='' -FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table. ",Verification,Conformance,Value,field_is_standard_valid_concept.sql,isStandardValidConcept=='Yes' -FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,measureValueCompleteness=='Yes' -FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,standardConceptRecordCompleteness=='Yes' -FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,sourceConceptRecordCompleteness=='Yes' -FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,sourceValueCompleteness=='Yes' -FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,plausibleValueLow!='' -FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,plausibleValueHigh!='' -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' -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!='' \ No newline at end of file +for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,DataQualityDashboard,measureConditionEraCompleteness=='Yes' +FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification.,Verification,Conformance,Relational,field_cdm_field.sql,DataQualityDashboard,cdmFieldName!='' +FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,DataQualityDashboard,isRequired=='Yes' +FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,DataQualityDashboard,cdmDatatype=='integer' +FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,DataQualityDashboard,isPrimaryKey=='Yes' +FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,DataQualityDashboard,isForeignKey=='Yes' +FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,DataQualityDashboard,isForeignKey=='Yes' & fkDomain!= '' +FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,DataQualityDashboard,isForeignKey=='Yes' & fkClass!='' +FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table.",Verification,Conformance,Value,field_is_standard_valid_concept.sql,DataQualityDashboard,isStandardValidConcept=='Yes' +FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,DataQualityDashboard,measureValueCompleteness=='Yes' +FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,standardConceptRecordCompleteness=='Yes' +FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,sourceConceptRecordCompleteness=='Yes' +FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,DataQualityDashboard,sourceValueCompleteness=='Yes' +FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,DataQualityDashboard,plausibleValueLow!='' +FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,DataQualityDashboard,plausibleValueHigh!='' +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,DataQualityDashboard,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,DataQualityDashboard,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,DataQualityDashboard,withinVisitDates=='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,DataQualityDashboard,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,DataQualityDashboard,plausibleUnitConceptIdsThreshold!='' diff --git a/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv b/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv index 22630353..c64f2c97 100644 --- a/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv +++ b/inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv @@ -1,24 +1,24 @@ -checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,evaluationFilter -TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification. ,Verification,Conformance,Relational,table_cdm_table.sql,cdmTableName!='' -TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,measurePersonCompleteness=='Yes' +checkLevel,checkName,checkDescription,kahnContext,kahnCategory,kahnSubcategory,sqlFile,packageName,evaluationFilter +TABLE,cdmTable,A yes or no value indicating if @cdmTableName table is present as expected based on the specification.,Verification,Conformance,Relational,table_cdm_table.sql,DataQualityDashboard,cdmTableName!='' +TABLE,measurePersonCompleteness,The number and percent of persons in the CDM that do not have at least one record in the @cdmTableName table,Validation,Completeness,,table_person_completeness.sql,DataQualityDashboard,measurePersonCompleteness=='Yes' TABLE,measureConditionEraCompleteness,"The number and Percent of persons that does not have condition_era built successfully -for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,measureConditionEraCompleteness=='Yes' -FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification. ,Verification,Conformance,Relational,field_cdm_field.sql,cdmFieldName!='' -FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,isRequired=='Yes' -FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,cdmDatatype=='integer' -FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,isPrimaryKey=='Yes' -FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,isForeignKey=='Yes' -FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,isForeignKey=='Yes' & fkDomain!= '' -FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,isForeignKey=='Yes' & fkClass!='' -FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table. ",Verification,Conformance,Value,field_is_standard_valid_concept.sql,isStandardValidConcept=='Yes' -FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,measureValueCompleteness=='Yes' -FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,standardConceptRecordCompleteness=='Yes' -FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,sourceConceptRecordCompleteness=='Yes' -FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,sourceValueCompleteness=='Yes' -FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,plausibleValueLow!='' -FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,plausibleValueHigh!='' -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' -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!='' \ No newline at end of file +for all persons in condition_occurrence",Validation,Completeness,,table_condition_era_completeness.sql,DataQualityDashboard,measureConditionEraCompleteness=='Yes' +FIELD,cdmField,A yes or no value indicating if @cdmFieldName is present in the @cdmTableName table as expected based on the specification.,Verification,Conformance,Relational,field_cdm_field.sql,DataQualityDashboard,cdmFieldName!='' +FIELD,isRequired,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName that is considered not nullable.,Validation,Conformance,Relational,field_is_not_nullable.sql,DataQualityDashboard,isRequired=='Yes' +FIELD,cdmDatatype,A yes or no value indicating if the @cdmFieldName in the @cdmTableName is the expected data type based on the specification.,Verification,Conformance,Value,field_cdm_datatype.sql,DataQualityDashboard,cdmDatatype=='integer' +FIELD,isPrimaryKey,The number and percent of records that have a duplicate value in the @cdmFieldName field of the @cdmTableName.,Verification,Conformance,Relational,field_is_primary_key.sql,DataQualityDashboard,isPrimaryKey=='Yes' +FIELD,isForeignKey,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that does not exist in the @fkTableName table.,Verification,Conformance,Relational,is_foreign_key.sql,DataQualityDashboard,isForeignKey=='Yes' +FIELD,fkDomain,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkDomain domain.,Verification,Conformance,Value,field_fk_domain.sql,DataQualityDashboard,isForeignKey=='Yes' & fkDomain!= '' +FIELD,fkClass,The number and percent of records that have a value in the @cdmFieldName field in the @cdmTableName table that do not conform to the @fkClass class.,Verification,Conformance,Computational,field_fk_class.sql,DataQualityDashboard,isForeignKey=='Yes' & fkClass!='' +FIELD,isStandardValidConcept,"The number and percent of records that do not have a standard, valid concept in the @cdmFieldName field in the @cdmTableName table.",Verification,Conformance,Value,field_is_standard_valid_concept.sql,DataQualityDashboard,isStandardValidConcept=='Yes' +FIELD,measureValueCompleteness,The number and percent of records with a NULL value in the @cdmFieldName of the @cdmTableName.,Verification,Completeness,,field_measure_value_completeness.sql,DataQualityDashboard,measureValueCompleteness=='Yes' +FIELD,standardConceptRecordCompleteness,The number and percent of records with a value of 0 in the standard concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,standardConceptRecordCompleteness=='Yes' +FIELD,sourceConceptRecordCompleteness,The number and percent of records with a value of 0 in the source concept field @cdmFieldName in the @cdmTableName table.,Verification,Completeness,,field_concept_record_completeness.sql,DataQualityDashboard,sourceConceptRecordCompleteness=='Yes' +FIELD,sourceValueCompleteness,The number and percent of distinct source values in the @cdmFieldName field of the @cdmTableName table mapped to 0.,Verification,Completeness,,field_source_value_completeness.sql,DataQualityDashboard,sourceValueCompleteness=='Yes' +FIELD,plausibleValueLow,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table less than @plausibleValueLow.,Verification,Plausibility,Atemporal,field_plausible_value_low.sql,DataQualityDashboard,plausibleValueLow!='' +FIELD,plausibleValueHigh,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName table greater than @plausibleValueHigh.,Verification,Plausibility,Atemporal,field_plausible_value_high.sql,DataQualityDashboard,plausibleValueHigh!='' +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,DataQualityDashboard,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,DataQualityDashboard,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,DataQualityDashboard,withinVisitDates=='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,DataQualityDashboard,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,DataQualityDashboard,plausibleUnitConceptIdsThreshold!='' diff --git a/man/dot-writeResultsToCsv.Rd b/man/dot-writeResultsToCsv.Rd index 96cb0a4a..245a4c5c 100644 --- a/man/dot-writeResultsToCsv.Rd +++ b/man/dot-writeResultsToCsv.Rd @@ -7,12 +7,12 @@ .writeResultsToCsv( checkResults, csvPath, - columns = c("checkId", "FAILED", "PASSED", "IS_ERROR", "NOT_APPLICABLE", "CHECK_NAME", - "CHECK_DESCRIPTION", "THRESHOLD_VALUE", "NOTES_VALUE", "CHECK_LEVEL", "CATEGORY", - "SUBCATEGORY", "CONTEXT", "CHECK_LEVEL", "CDM_TABLE_NAME", "CDM_FIELD_NAME", - "CONCEPT_ID", "UNIT_CONCEPT_ID", "NUM_VIOLATED_ROWS", "PCT_VIOLATED_ROWS", - "NUM_DENOMINATOR_ROWS", "EXECUTION_TIME", "NOT_APPLICABLE_REASON", "ERROR", - "QUERY_TEXT"), + columns = c("checkId", "FAILED", "PASSED", "IS_ERROR", "NOT_APPLICABLE", + "CHECK_NAME", "CHECK_DESCRIPTION", "THRESHOLD_VALUE", "NOTES_VALUE", "CHECK_LEVEL", + "CATEGORY", "SUBCATEGORY", "CONTEXT", "CHECK_LEVEL", "CDM_TABLE_NAME", + "CDM_FIELD_NAME", "CONCEPT_ID", "UNIT_CONCEPT_ID", "NUM_VIOLATED_ROWS", + "PCT_VIOLATED_ROWS", "NUM_DENOMINATOR_ROWS", "EXECUTION_TIME", + "NOT_APPLICABLE_REASON", "ERROR", "QUERY_TEXT"), delimiter = "," ) } diff --git a/man/executeDqChecks.Rd b/man/executeDqChecks.Rd index 3b752b06..473837c2 100644 --- a/man/executeDqChecks.Rd +++ b/man/executeDqChecks.Rd @@ -28,7 +28,8 @@ executeDqChecks( cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", - conceptCheckThresholdLoc = "default" + conceptCheckThresholdLoc = "default", + systemFileNamespace = "DataQualityDashboard" ) } \arguments{ @@ -79,6 +80,8 @@ with the fields cohort_definition_id and subject_id.} \item{fieldCheckThresholdLoc}{The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.} \item{conceptCheckThresholdLoc}{The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.} + +\item{systemFileNamespace}{The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.} } \value{ If sqlOnly = FALSE, a list object of results diff --git a/man/listDqChecks.Rd b/man/listDqChecks.Rd index b6fc60e4..979c6799 100644 --- a/man/listDqChecks.Rd +++ b/man/listDqChecks.Rd @@ -8,7 +8,8 @@ listDqChecks( cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", - conceptCheckThresholdLoc = "default" + conceptCheckThresholdLoc = "default", + systemFileNamespace = "DataQualityDashboard" ) } \arguments{ @@ -19,6 +20,8 @@ listDqChecks( \item{fieldCheckThresholdLoc}{The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.} \item{conceptCheckThresholdLoc}{The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.} + +\item{systemFileNamespace}{The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.} } \description{ Details on all checks defined by the DataQualityDashboard Package. diff --git a/man/reEvaluateThresholds.Rd b/man/reEvaluateThresholds.Rd index 47605739..12879f8f 100644 --- a/man/reEvaluateThresholds.Rd +++ b/man/reEvaluateThresholds.Rd @@ -11,7 +11,8 @@ reEvaluateThresholds( tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", conceptCheckThresholdLoc = "default", - cdmVersion = "5.3" + cdmVersion = "5.3", + systemFileNamespace = "DataQualityDashboard" ) } \arguments{ @@ -28,6 +29,8 @@ reEvaluateThresholds( \item{conceptCheckThresholdLoc}{The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.} \item{cdmVersion}{The CDM version to target for the data source. By default, 5.3 is used.} + +\item{systemFileNamespace}{The name of the package where the check are stored. If not specified the default `DataQualityDashboard` namespace will be applied.} } \description{ Re-evaluate an existing DQD result against an updated thresholds file. diff --git a/man/writeJsonResultsToCsv.Rd b/man/writeJsonResultsToCsv.Rd index 5e0211e5..e552e040 100644 --- a/man/writeJsonResultsToCsv.Rd +++ b/man/writeJsonResultsToCsv.Rd @@ -7,12 +7,12 @@ writeJsonResultsToCsv( jsonPath, csvPath, - columns = c("checkId", "FAILED", "PASSED", "IS_ERROR", "NOT_APPLICABLE", "CHECK_NAME", - "CHECK_DESCRIPTION", "THRESHOLD_VALUE", "NOTES_VALUE", "CHECK_LEVEL", "CATEGORY", - "SUBCATEGORY", "CONTEXT", "CHECK_LEVEL", "CDM_TABLE_NAME", "CDM_FIELD_NAME", - "CONCEPT_ID", "UNIT_CONCEPT_ID", "NUM_VIOLATED_ROWS", "PCT_VIOLATED_ROWS", - "NUM_DENOMINATOR_ROWS", "EXECUTION_TIME", "NOT_APPLICABLE_REASON", "ERROR", - "QUERY_TEXT"), + columns = c("checkId", "FAILED", "PASSED", "IS_ERROR", "NOT_APPLICABLE", + "CHECK_NAME", "CHECK_DESCRIPTION", "THRESHOLD_VALUE", "NOTES_VALUE", "CHECK_LEVEL", + "CATEGORY", "SUBCATEGORY", "CONTEXT", "CHECK_LEVEL", "CDM_TABLE_NAME", + "CDM_FIELD_NAME", "CONCEPT_ID", "UNIT_CONCEPT_ID", "NUM_VIOLATED_ROWS", + "PCT_VIOLATED_ROWS", "NUM_DENOMINATOR_ROWS", "EXECUTION_TIME", + "NOT_APPLICABLE_REASON", "ERROR", "QUERY_TEXT"), delimiter = "," ) }