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Creates a mock CDM database populated with various vocabulary tables.

Source: R/mockVocabulary.R
mockVocabularyTables.Rd

[Experimental]

Usage

mockVocabularyTables(
  cdm = mockCdmReference(),
  vocabularySet = "mock",
  cdmSource = NULL,
  concept = NULL,
  vocabulary = NULL,
  conceptRelationship = NULL,
  conceptSynonym = NULL,
  conceptAncestor = NULL,
  drugStrength = NULL,
  conceptSet = NULL,
  includeRelated = TRUE,
  keepDomains = c("Unit", "Visit", "Gender")
)

Arguments

cdm

A local cdm_reference object used as the base structure to update.

vocabularySet

A character string specifying the name of the vocabulary set to be used when creating the vocabulary tables for the CDM. Options are "mock" or "eunomia":

  • "mock": Provides a very small synthetic vocabulary subset, suitable for tests that do not require realistic vocabulary names or relationships.

  • "eunomia": Uses the vocabulary from the Eunomia test database, which contains real vocabularies available from ATHENA.

cdmSource

An optional data frame representing the CDM source table. If provided, it will be used directly; otherwise, a mock table will be generated based on the vocabularySet prefix.

concept

An optional data frame representing the concept table. If provided, it will be used directly; if NULL, a mock table will be generated.

vocabulary

An optional data frame representing the vocabulary table. If provided, it will be used directly; if NULL, a mock table will be generated.

conceptRelationship

An optional data frame representing the concept relationship table. If provided, it will be used directly; if NULL, a mock table will be generated.

conceptSynonym

An optional data frame representing the concept synonym table. If provided, it will be used directly; if NULL, a mock table will be generated.

conceptAncestor

An optional data frame representing the concept ancestor table. If provided, it will be used directly; if NULL, a mock table will be generated.

drugStrength

An optional data frame representing the drug strength table. If provided, it will be used directly; if NULL, a mock table will be generated.

conceptSet

An optional numeric vector of concept IDs used to subset the vocabulary after it has been assembled. When supplied, the function keeps the requested concepts and directly related vocabulary rows such as synonyms, relationships, ancestors, and drug strength records.

includeRelated

Whether to retain vocabulary concepts directly related to conceptSet. Defaults to TRUE. If FALSE, only the requested concept IDs are kept.

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.

Details

This function adds specified vocabulary tables to a CDM object. It can either populate the tables with provided data frames or initialize empty tables if no data is provided. This is useful for setting up a testing environment with controlled vocabulary data.

Examples

library(omock)

# Create a mock CDM reference and populate it with mock vocabulary tables
cdm <- mockCdmReference() |> mockVocabularyTables(vocabularySet = "mock")

# View the names of the tables added to the CDM
names(cdm)
#> [1] "person"               "observation_period"   "cdm_source"          
#> [4] "concept"              "vocabulary"           "concept_relationship"
#> [7] "concept_synonym"      "concept_ancestor"     "drug_strength"