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How to Use CohortGenerator with CohortDiagnostics?

General
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#1

Hi @anthonysena , @schuemie , and @Gowtham_Rao

Anthony and Martijn, I love CohortGenerator!
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 CohortDiagnostics.

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.

Process Using CohortGenerator

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)

Utilizing my cohortDefinitionSet per CohortGenerator, I save my cohort appropriately based on the CohortGenerator tutorial:

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 DatabaseConnector.
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"
)

Now using 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 CohortGenerator:

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 CohortDiagnostics!

Process for Utilizing CohortDiagnostics

After reading through the documentation for CohortDiagnostics, I surmised that one could do this after generating a cohort with CohortGenerator:

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.

Conclusion

I think 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!

Thanks!

~ tcp :deciduous_tree:

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
#2

Hi @TheCedarPrince ! Thanks for your enthusiasm. You are right that right now CohortDiagnostics does play nicely with CohortGenerator. We’re furiously working on a release that is specifically focused on this. (You can take a peek at the CohortGeneratorDependency branch until then).

1 Like
#3

This is wonderful to hear!
@schuemie , I took a look at the branch and read through some of the Rmd documentation and I would be happy to assist if possible in the development.
Happy to chat further!
Thanks!

t