Custom CovariateData Builder

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Custom CovariateData Builder — Eunomia Demo

This vignette demonstrates how to use OdysseusCharacterizationModule as a custom covariate builder for the FeatureExtraction package. When you pass an OCM covariate settings object to FeatureExtraction::getDbCovariateData(), it returns a standard CovariateData (Andromeda) object that plugs directly into CohortMethod, PatientLevelPrediction, or any other HADES package that consumes covariates.

Prerequisites

for (pkg in c("DatabaseConnector", "Eunomia", "Andromeda")) {
  if (!requireNamespace(pkg, quietly = TRUE)) install.packages(pkg)
}

library(OdysseusCharacterizationModule)
library(DatabaseConnector)
library(Eunomia)

1. Connect to Eunomia

connectionDetails <- getEunomiaConnectionDetails()
Eunomia::createCohorts(connectionDetails)
connection <- connect(connectionDetails)

COHORT_ID  <- 1L          # Celecoxib new users
CDM_SCHEMA <- "main"

2. Create covariate settings

createOcmCovariateSettings() accepts the same parameters as planAnalysis() — analysis windows, base features, cohort features, and concept-set features. The object it returns carries an attribute fun that tells FeatureExtraction which builder function to call.

ocmSettings <- createOcmCovariateSettings(
  analysisWindows = defineAnalysisWindows(
    startDays = c(-365),
    endDays   = c(-1)
  ),
  useBaseFeatures = list(
    condition_occurrence = list(include = TRUE, type = "start"),
    drug_exposure        = list(include = TRUE, atc = FALSE),
    condition_era        = list(include = FALSE),
    drug_era             = list(include = FALSE),
    procedure_occurrence = list(include = FALSE),
    observation          = list(include = FALSE),
    device_exposure      = list(include = FALSE),
    visit_occurrence     = list(include = FALSE),
    measurement          = list(include = FALSE)
  )
)

class(ocmSettings)
#> [1] "covariateSettings"

attr(ocmSettings, "fun")
#> [1] "getDbOcmCovariateData"

3. Standalone usage — call the builder directly

You do not need FeatureExtraction installed to use the builder. getDbOcmCovariateData() runs the full OCM pipeline and assembles a CovariateData Andromeda object.

covData <- getDbOcmCovariateData(
  connection        = connection,
  cdmDatabaseSchema = CDM_SCHEMA,
  cohortTable       = "main.cohort",
  cohortIds         = c(COHORT_ID),
  rowIdField        = "subject_id",
  covariateSettings = ocmSettings,
  aggregated        = FALSE
)

Inspect the covariates table

Each row is a sparse (rowId, covariateId, covariateValue) triple. covariateValue is 1 for binary features.

covDf <- covData$covariates |> as.data.frame()
cat("Total covariate entries:", nrow(covDf), "\n")
cat("Unique patients:",        length(unique(covDf$rowId)), "\n")
cat("Unique covariates:",      length(unique(covDf$covariateId)), "\n")
head(covDf)

Inspect the covariate reference

Maps each covariateId to a human-readable name, concept ID, and analysis ID.

refDf <- covData$covariateRef |> as.data.frame()
head(refDf, 10)

Inspect the analysis reference

One row per analysis describing the domain, time window, and whether the covariate is binary.

analysisDf <- covData$analysisRef |> as.data.frame()
analysisDf

Andromeda::close(covData)

4. FeatureExtraction integration

When FeatureExtraction is available, pass ocmSettings as covariateSettings. FeatureExtraction reads the fun attribute, calls getDbOcmCovariateData() internally, and returns the result as a standard CovariateData object.

if (requireNamespace("FeatureExtraction", quietly = TRUE)) {

  covDataFE <- FeatureExtraction::getDbCovariateData(
    connection            = connection,
    cdmDatabaseSchema     = CDM_SCHEMA,
    cohortDatabaseSchema  = CDM_SCHEMA,
    cohortTable           = "cohort",
    cohortIds             = c(COHORT_ID),
    covariateSettings     = ocmSettings,
    aggregated            = FALSE
  )

  cat("Covariates (via FE):", nrow(as.data.frame(covDataFE$covariates)), "\n")
  Andromeda::close(covDataFE)

} else {
  message("FeatureExtraction not installed — skipping integration demo.")
}

5. Combining with standard FeatureExtraction covariates

A key benefit of the custom builder pattern is that you can combine OCM covariates with FeatureExtraction’s built-in covariates. Pass a list of settings objects:

if (requireNamespace("FeatureExtraction", quietly = TRUE)) {

  feSettings <- FeatureExtraction::createCovariateSettings(
    useDemographicsGender    = TRUE,
    useDemographicsAge       = TRUE,
    useDemographicsIndexYear = TRUE
  )

  combinedCovData <- FeatureExtraction::getDbCovariateData(
    connection            = connection,
    cdmDatabaseSchema     = CDM_SCHEMA,
    cohortDatabaseSchema  = CDM_SCHEMA,
    cohortTable           = "cohort",
    cohortIds             = c(COHORT_ID),
    covariateSettings     = list(feSettings, ocmSettings),
    aggregated            = FALSE
  )

  covDf <- as.data.frame(combinedCovData$covariates)
  cat("Total covariate entries (combined):", nrow(covDf), "\n")
  cat("Unique covariates (combined):",      length(unique(covDf$covariateId)), "\n")

  Andromeda::close(combinedCovData)

} else {
  message("FeatureExtraction not installed — skipping combined demo.")
}

6. Multiple domains and time windows

ocmSettingsWide <- createOcmCovariateSettings(
  analysisWindows = defineAnalysisWindows(
    startDays = c(-365, -30, 1),
    endDays   = c(-1,   -1, 30)
  ),
  useBaseFeatures = list(
    condition_occurrence = list(include = TRUE, type = "start"),
    drug_exposure        = list(include = TRUE, atc = FALSE),
    procedure_occurrence = list(include = TRUE),
    condition_era        = list(include = FALSE),
    drug_era             = list(include = FALSE),
    observation          = list(include = FALSE),
    device_exposure      = list(include = FALSE),
    visit_occurrence     = list(include = TRUE, type = "start"),
    measurement          = list(include = TRUE)
  )
)

covDataWide <- getDbOcmCovariateData(
  connection        = connection,
  cdmDatabaseSchema = CDM_SCHEMA,
  cohortTable       = "main.cohort",
  cohortIds         = c(COHORT_ID),
  covariateSettings = ocmSettingsWide,
  aggregated        = FALSE
)

cat("Analyses:",   nrow(as.data.frame(covDataWide$analysisRef)), "\n")
cat("Covariates:", nrow(as.data.frame(covDataWide$covariates)), "\n")

Andromeda::close(covDataWide)

7. Using concept-set features

Define a custom concept set (e.g. hypertension-related conditions) and extract it as a binary covariate:

ocmConceptSet <- createOcmCovariateSettings(
  analysisWindows = defineAnalysisWindows(
    startDays = c(-365),
    endDays   = c(-1)
  ),
  useBaseFeatures = list(
    condition_occurrence = list(include = FALSE),
    condition_era        = list(include = FALSE),
    drug_exposure        = list(include = FALSE),
    drug_era             = list(include = FALSE),
    procedure_occurrence = list(include = FALSE),
    observation          = list(include = FALSE),
    device_exposure      = list(include = FALSE),
    visit_occurrence     = list(include = FALSE),
    measurement          = list(include = FALSE)
  ),
  useConceptSetFeatures = list(
    include = TRUE,
    type    = "binary",
    conceptSets = list(
      hypertension = list(
        items = list(
          list(
            concept            = list(CONCEPT_ID = 316866L),
            includeDescendants = TRUE,
            includeMapped      = FALSE,
            isExcluded         = FALSE
          )
        ),
        tables = c("condition_occurrence")
      )
    )
  )
)

covDataCS <- getDbOcmCovariateData(
  connection        = connection,
  cdmDatabaseSchema = CDM_SCHEMA,
  cohortTable       = "main.cohort",
  cohortIds         = c(COHORT_ID),
  covariateSettings = ocmConceptSet,
  aggregated        = FALSE
)

cat("Concept-set covariates:", nrow(as.data.frame(covDataCS$covariates)), "\n")
as.data.frame(covDataCS$covariateRef)

Andromeda::close(covDataCS)

Cleanup

disconnect(connection)

Summary

Function	Purpose
`createOcmCovariateSettings()`	Configure OCM features as a `covariateSettings` object
`getDbOcmCovariateData()`	Execute the pipeline and return a `CovariateData` Andromeda object
`FeatureExtraction::getDbCovariateData(..., covariateSettings = ocmSettings)`	Use OCM as a plug-in builder inside FeatureExtraction

The returned CovariateData object contains:

covariates — sparse (rowId, covariateId, covariateValue) table
covariateRef — covariate metadata (name, concept ID, analysis ID)
analysisRef — analysis metadata (domain, time window, binary flag)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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