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schuemie
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| # Unit tests on CohortDiagnostics using testing servers take too long, so using local | ||
| # Postgres server | ||
| library(dplyr) | ||
| library(Capr) | ||
|
|
||
| connectionDetails <- DatabaseConnector::createConnectionDetails( | ||
| dbms = "postgresql", | ||
| user = Sys.getenv("LOCAL_POSTGRES_USER"), | ||
| password = Sys.getenv("LOCAL_POSTGRES_PASSWORD"), | ||
| server = Sys.getenv("LOCAL_POSTGRES_SERVER") | ||
| ) | ||
| cdmDatabaseSchema <- Sys.getenv("LOCAL_POSTGRES_CDM_SCHEMA") | ||
| cohortDatabaseSchema <- Sys.getenv("LOCAL_POSTGRES_OHDSI_SCHEMA") | ||
| cohortTable <- "cd_test" | ||
| folder <- "e:/temp/cdOutput" | ||
|
|
||
| # Create cohorts using Capr ---------------------------------------------------- | ||
| osteoArthritisOfKneeConceptId <- 4079750 | ||
| celecoxibConceptId <- 1118084 | ||
| diclofenacConceptId <- 1124300 | ||
| osteoArthritisOfKnee <- cs( | ||
| descendants(osteoArthritisOfKneeConceptId), | ||
| name = "Osteoarthritis of knee" | ||
| ) | ||
| attrition = attrition( | ||
| "prior osteoarthritis of knee" = withAll( | ||
| atLeast(1, conditionOccurrence(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0))) | ||
| ) | ||
| ) | ||
| celecoxib <- cs( | ||
| descendants(celecoxibConceptId), | ||
| name = "Celecoxib" | ||
| ) | ||
| diclofenac <- cs( | ||
| descendants(diclofenacConceptId), | ||
| name = "Diclofenac" | ||
| ) | ||
| celecoxibCohort <- cohort( | ||
| entry = entry( | ||
| drugExposure(celecoxib, firstOccurrence()), | ||
| observationWindow = continuousObservation(priorDays = 365) | ||
| ), | ||
| # attrition = attrition, | ||
| exit = exit(endStrategy = drugExit(celecoxib, | ||
| persistenceWindow = 30, | ||
| surveillanceWindow = 0)) | ||
| ) | ||
| diclofenacCohort <- cohort( | ||
| entry = entry( | ||
| drugExposure(diclofenac, firstOccurrence()), | ||
| observationWindow = continuousObservation(priorDays = 365) | ||
| ), | ||
| # attrition = attrition, | ||
| exit = exit(endStrategy = drugExit(diclofenac, | ||
| persistenceWindow = 30, | ||
| surveillanceWindow = 0)) | ||
| ) | ||
| cohortDefinitionSet <- Capr::makeCohortSet(celecoxibCohort, diclofenacCohort) | ||
|
|
||
| # Generate cohorts ------------------------------------------------------------- | ||
| cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable) | ||
| CohortGenerator::createCohortTables( | ||
| connectionDetails = connectionDetails, | ||
| cohortTableNames = cohortTableNames, | ||
| cohortDatabaseSchema = cohortDatabaseSchema, | ||
| incremental = FALSE | ||
| ) | ||
| CohortGenerator::generateCohortSet( | ||
| connectionDetails = connectionDetails, | ||
| cdmDatabaseSchema = cdmDatabaseSchema, | ||
| cohortDatabaseSchema = cohortDatabaseSchema, | ||
| cohortTableNames = cohortTableNames, | ||
| cohortDefinitionSet = cohortDefinitionSet, | ||
| incremental = FALSE | ||
| ) | ||
| CohortGenerator::getCohortCounts(connectionDetails = connectionDetails, | ||
| cohortDatabaseSchema = cohortDatabaseSchema, | ||
| cohortTable = cohortTable) | ||
|
|
||
| # Run CohortDiagnostics -------------------------------------------------------- | ||
| dir.create(folder) | ||
|
|
||
| cohortDefinitionSet$cohortId <- as.double(cohortDefinitionSet$cohortId) | ||
| CohortDiagnostics::executeDiagnostics( | ||
| cohortDefinitionSet = cohortDefinitionSet, | ||
| connectionDetails = connectionDetails, | ||
| cdmDatabaseSchema = cdmDatabaseSchema, | ||
| cohortDatabaseSchema = cohortDatabaseSchema, | ||
| cohortTable = cohortTable, | ||
| cohortIds = cohortDefinitionSet$cohortId, | ||
| exportFolder = file.path(folder, "export"), | ||
| databaseId = "Synpuf", | ||
| runInclusionStatistics = TRUE, | ||
| runBreakdownIndexEvents = TRUE, | ||
| runTemporalCohortCharacterization = TRUE, | ||
| runIncidenceRate = TRUE, | ||
| runIncludedSourceConcepts = TRUE, | ||
| runOrphanConcepts = TRUE, | ||
| runTimeSeries = TRUE, | ||
| runCohortRelationship = TRUE, | ||
| minCellCount = 5, | ||
| ) | ||
|
|
||
| file.exists(file.path( | ||
| folder, "export", paste0("Results_Synpuf.zip") | ||
| )) |
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