Anthony and Martijn, I love
You released it at the perfect time for my work and ongoing study!
Currently, I went through the tutorial which was very straightforward to do!
However, what I am having trouble with doing is how to take my generated cohort and use it in
In the following sections, I go through my process of creating cohorts via
CohortGenerator, then my attempt at utilizing these cohorts in
CohortDiagnostics, and then final concluding thoughts.
First, I load the libraries needed
library("CohortGenerator") # Used for generating cohort library("DatabaseConnector") # Connecting to OMOP Database library("ROhdsiWebApi") # Used for ATLAS connection
Then I grab my ATLAS cohort definition from the public ATLAS Demo instance:
ATLASurl <- "http://api.ohdsi.org:8080/WebAPI" cohortID <- c(1778180) cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(baseUrl = ATLASurl, cohortIds = cohortID, generateStats = TRUE)
CohortGenerator, I save my cohort appropriately based on the
saveCohortDefinitionSet(cohortDefinitionSet = cohortDefinitionSet, settingsFolder = file.path("inst/settings"), jsonFolder = file.path("inst/cohorts"), sqlFolder = file.path("inst/sql/sql_server"))
Then, I connect to my database via
The exact details redacted so just trust me when I say the connection does in fact work:
connectionDetails <- DatabaseConnector::createConnectionDetails( dbms = "postgresql", server = "server", user = "user", password = "password", port = 1234, pathToDriver = "utils" )
CohortGenerator, I can generate my cohorts appropriately:
cohortTableNames <- getCohortTableNames(cohortTable = "cg_example") createCohortTables(connectionDetails = connectionDetails, cohortTableNames = cohortTableNames, cohortDatabaseSchema = "test") generateCohortSet(connectionDetails= connectionDetails, cdmDatabaseSchema = "schema", cohortDatabaseSchema = "test", cohortTableNames = cohortTableNames, cohortDefinitionSet = cohortDefinitionSet)
Additionally, I can now build statistics utilizing
insertInclusionRuleNames(connectionDetails = connectionDetails, cohortDefinitionSet = cohortDefinitionSet, cohortDatabaseSchema = "test", cohortInclusionTable = cohortTableNames$cohortInclusionTable) exportCohortStatsTables(connectionDetails = connectionDetails, cohortDatabaseSchema = "test", cohortTableNames = cohortTableNames, cohortStatisticsFolder = file.path("inst/InclusionStats"))
Now I am in theory ready to utilize
After reading through the documentation for
CohortDiagnostics, I surmised that one could do this after generating a cohort with
library("CohortDiagnostics") runCohortDiagnostics( packageName = "SUPREME-DM", cohortToCreateFile = "CohortsToCreate.csv", baseUrl = NULL, cohortSetReference = NULL, connectionDetails = connectionDetails, connection = NULL, cdmDatabaseSchema = "schema", oracleTempSchema = NULL, tempEmulationSchema = "tmp", cohortDatabaseSchema = "test", vocabularyDatabaseSchema = "schema", cohortTable = "stats_example", cohortIds = NULL, inclusionStatisticsFolder = NULL, exportFolder = "testdiagnostics", databaseId = "ID", databaseName = NULL, databaseDescription = NULL, cdmVersion = 5, runInclusionStatistics = FALSE, runIncludedSourceConcepts = TRUE, runOrphanConcepts = TRUE, runTimeDistributions = TRUE, runVisitContext = TRUE, runBreakdownIndexEvents = TRUE, runIncidenceRate = TRUE, runTimeSeries = FALSE, runCohortOverlap = FALSE, runCohortCharacterization = TRUE, covariateSettings = createDefaultCovariateSettings(), runTemporalCohortCharacterization = TRUE, temporalCovariateSettings = createTemporalCovariateSettings(useConditionOccurrence = TRUE, useDrugEraStart = TRUE, useProcedureOccurrence = TRUE, useMeasurement = TRUE, temporalStartDays = c(-365, -30, 0, 1, 31), temporalEndDays = c(-31, -1, 0, 30, 365)), minCellCount = 5, incremental = FALSE, incrementalFolder = NULL )
Yet when I run this, I get the following error that I do not know how to debug:
Run Cohort Diagnostics started at 2022-01-05 11:42:40 Created folder at testdiagnostics Error: '' does not exist in current working directory ('/Projects/ PhenoEx/demos/ohdsi-r').
I do not know what this inscrutable error means and I have spent several hours trying to debug it.
CohortGenerator could honestly become the de facto tool used in the HADES environment to provide a standard interface to the rest of the HADES ecosystem.
I just need a bit of help to satisfy the interface using it to the other packages.
Any thoughts or help here would be much appreciated!
P.S. Here are my package versions:
Package Version Andromeda Andromeda 0.5.0 CohortDiagnostics CohortDiagnostics 2.1.4 CohortGenerator CohortGenerator 0.2.0 DatabaseConnector DatabaseConnector 5.0.0 FeatureExtraction FeatureExtraction 3.2.0 rJava rJava 1.0-6 rlang rlang 0.4.12 ROhdsiWebApi ROhdsiWebApi 1.3.0 SqlRender SqlRender 1.8.1