Skip to contents

Creates a mock CDM database populated with various vocabulary tables.

Source: R/mockVocabulary.R
mockVocabularyTables.Rd

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.

Usage

mockVocabularyTables(
  cdm = mockCdmReference(),
  vocabularySet = "mock",
  cdmSource = NULL,
  concept = NULL,
  vocabulary = NULL,
  conceptRelationship = NULL,
  conceptSynonym = NULL,
  conceptAncestor = NULL,
  drugStrength = NULL
)

Arguments

cdm

A cdm_reference object that serves as the base structure for adding vocabulary tables. This should be an existing or a newly created CDM object, typically initialized without any vocabulary tables.

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.

Value

Returns the modified cdm object with the new or provided vocabulary tables added.

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"