OHDSI / OHDSI/Characterization

Characterization is not supporting temporal covariate settings object

Open
#13 2 comments 0 reactions 1 assignee View on GitHub

@jreps is already working on this.

Since Apr 26, 2024.

Dominant language
R
Stars
3
Forks
6
Avg merge
2h 11m
Merged PRs (30d)
4

Description

Reproducible code. the code below gives the error
Error: Columns time_id not found

While uploading covariates

This is because timeId is absent in these tables
https://github.com/OHDSI/Characterization/blob/fa8c856802d75ae1e9289af11490830d39e5465e/inst/sql/sql_server/ResultTables.sql#L99-L123

# Set up
remotes::install_github("OHDSI/DatabaseConnector")
remotes::install_github("OHDSI/FeatureExtraction")

outputLocation <- file.path("D:", "test")

# cohort definition set
targetCohortIds <- 40 # diabetes mellitus
outcomeCohortIds <- 23 # inpatient
cohortDefinitionSet <-
  PhenotypeLibrary::getPlCohortDefinitionSet(cohortIds = c(targetCohortIds, outcomeCohortIds))

database <- "eunomia"
resultsLocation <- file.path(outputLocation, database)
cohortDatabaseSchema <- "main"
cdmDatabaseSchema <- "main"
databaseId <- database
cohortTableNames <-
  CohortGenerator::getCohortTableNames(cohortTable = "cohort")
targetCohortDatabaseSchema <- cdmDatabaseSchema
targetCohortTable <- cohortTableNames$cohortTable
outcomeCohortDatabaseSchema <- cdmDatabaseSchema
outcomeCohortTable <- cohortTableNames$cohortTable
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
CohortGenerator::createCohortTables(
  connectionDetails = connectionDetails,
  cohortDatabaseSchema = cohortDatabaseSchema,
  cohortTableNames = cohortTableNames
)
CohortGenerator::generateCohortSet(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = cdmDatabaseSchema,
  cohortDatabaseSchema = cohortDatabaseSchema,
  cohortTableNames = cohortTableNames,
  cohortDefinitionSet = cohortDefinitionSet
)

# feature extraction specification from CohortDiagnostics as it has temporalCovariateSettings
cohortDiagnosticsCovariateSettings <-
  CohortDiagnostics::getDefaultCovariateSettings()


# Setting for characterization package
aggregateCovariateSettings1 <-
  Characterization::createAggregateCovariateSettings(
    targetIds = targetCohortIds,
    outcomeIds = outcomeCohortIds,
    riskWindowStart = 0,
    startAnchor = 'cohort start',
    riskWindowEnd = 0,
    endAnchor = 'cohort end',
    covariateSettings = cohortDiagnosticsCovariateSettings
  )

timeToEventSettings1 <- Characterization::createTimeToEventSettings(targetIds = targetCohortIds,
                                                                    outcomeIds = outcomeCohortIds)
dechallengeRechallengeSettings <-
  Characterization::createDechallengeRechallengeSettings(
    targetIds = targetCohortIds,
    outcomeIds = outcomeCohortIds,
    dechallengeStopInterval = 30,
    dechallengeEvaluationWindow = 31
  )


characterizationSettings <-
  Characterization::createCharacterizationSettings(
    timeToEventSettings = list(timeToEventSettings1),
    dechallengeRechallengeSettings = list(dechallengeRechallengeSettings),
    aggregateCovariateSettings = list(aggregateCovariateSettings1)
  )

Characterization::runCharacterizationAnalyses(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = cdmDatabaseSchema,
  targetDatabaseSchema = targetCohortDatabaseSchema,
  targetTable = targetCohortTable,
  outcomeDatabaseSchema = outcomeCohortDatabaseSchema,
  outcomeTable = outcomeCohortTable,
  characterizationSettings = characterizationSettings,
  saveDirectory = resultsLocation,
  tablePrefix = 'c_',
  databaseId = databaseId
)


Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.