OHDSI / OHDSI/FeatureExtraction
Feature Extraction seems to return NA for timeId for temporalCovariate continuous covariates
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Description
reproducible example
# Get cohort json
cohortJson <- RJSONIO::fromJSON("https://raw.githubusercontent.com/OHDSI/SkeletonCohortDiagnosticsStudy/main/inst/cohorts/14907.json", digits = 23) %>%
RJSONIO::toJSON(digits = 23, pretty = TRUE)
# render cohort sql
cohortExpression <- CirceR::cohortExpressionFromJson(expressionJson = cohortJson)
genOp <- CirceR::createGenerateOptions(
cohortId = 1,
vocabularySchema = "@vocabulary_database_schema",
generateStats = FALSE)
cohortSql <- CirceR::buildCohortQuery(expression = cohortExpression, options = genOp)
# set up connections to eunomia
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
connection = DatabaseConnector::connect(connectionDetails = connectionDetails)
cdmDatabaseSchema <- "main"
cohortDatabaseSchema <- "main"
cohortTable <- "cohort"
databaseId <- "Eunomia"
# instantiate cohort
DatabaseConnector::renderTranslateExecuteSql(connection = connection,
sql = cohortSql,
cdm_database_schema = cdmDatabaseSchema,
vocabulary_database_schema = cohortDatabaseSchema,
target_database_schema = cohortDatabaseSchema,
target_cohort_table = cohortTable)
# set up temporal covariate settings object
temporalCovariateSettings = createTemporalCovariateSettings(
useConditionOccurrence = TRUE,
useDrugEraStart = TRUE,
useDrugEraOverlap = TRUE,
useVisitCount = TRUE,
useVisitConceptCount = TRUE,
useProcedureOccurrence = TRUE,
useMeasurement = TRUE,
temporalStartDays = c(-365, -30, 0, 1, 31,
seq(from = -421, to = -31, by = 30),
seq(from = 0, to = 390, by = 30)),
temporalEndDays = c(-31, -1, 0, 30, 365,
seq(from = -391, to = -1, by = 30),
seq(from = 30, to = 420, by = 30))
)
# execute feature extraction
featureExtractionOutput <-
FeatureExtraction::getDbCovariateData(
connection = connection,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
covariateSettings = temporalCovariateSettings,
aggregated = TRUE
)
# inspect returned object
featureExtractionOutput$covariatesContinuous
See timeId is NA

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Research direction
Reproduce the example using FeatureExtraction::getDbCovariateData and inspect the returned covariatesContinuous data, focusing on how temporal covariate timeId values are produced. Compare the temporal settings and generated output to determine why timeId is NA; done means the affected continuous covariates return the expected time identifiers.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100