Subset vocabulary tables in a CDM

Restricts the vocabulary tables in a cdm_reference to a target concept set while optionally retaining directly related concepts and selected domain_id values. Non-vocabulary OMOP tables are then filtered so rows that reference removed concepts are also dropped.

Usage

subsetVocabularyTables(
  cdm = NULL,
  conceptSet = NULL,
  cdmTables = NULL,
  includeRelated = TRUE,
  keepDomains = c("Unit", "Visit", "Gender")
)

Arguments

cdm

A cdm_reference object used as the base structure to update.

conceptSet

Numeric vector of concept IDs to retain.

cdmTables

Optional named list of vocabulary tables to subset instead of a full cdm_reference. This is mainly used internally.

includeRelated

Whether to retain concepts directly related to conceptSet. Defaults to TRUE.

keepDomains

Character vector of domain_id values to always retain when subsetting vocabulary tables. Defaults to c("Unit", "Visit", "Gender").

Value

A modified cdm_reference object.

Examples

# \donttest{
cdm <- mockCdmFromDataset()
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
cdm <- cdm |> subsetVocabularyTables(conceptSet = c(35208414))
# }