Adds mock concept data to a concept table within a Common Data Model (CDM) object.

Usage

mockConcepts(cdm, conceptSet, domain = "Condition", seed = NULL)

Arguments

cdm: A local cdm_reference object used as the base structure to update.
conceptSet: A numeric vector of concept IDs to be added or updated in the concept table.These IDs should be unique within the context of the provided domain to avoid unintended overwriting unless that is the intended effect.
domain: A character string specifying the domain of the concepts being added.Only accepts "Condition", "Drug", "Measurement", or "Observation". This defines under which category the concepts fall and affects which vocabulary is used for them.
seed: An optional integer used to set the random seed for reproducibility. If NULL, the seed is not set.

Value

A modified cdm_reference object.

Details

This function inserts new concept entries into a specified domain within the concept table of a CDM object.It supports four domains: Condition, Drug, Measurement, and Observation. Existing entries with the same concept IDs will be overwritten, so caution should be used when adding data to prevent unintended data loss.

Examples

library(omock)
library(dplyr)

# Create a mock CDM reference and add concepts in the 'Condition' domain
cdm <- mockCdmReference() |> mockConcepts(
  conceptSet = c(100, 200), domain = "Condition"
)
#> Warning: `mockConcepts()` was deprecated in omock 0.6.2.9000.
#> ℹ `mockConcepts()` creates placeholder concept rows that may be mistaken for
#>   real OMOP vocabulary content. Use `mockCdmReference()` with `vocabularySet =
#>   "eunomia"`, `mockVocabularyTables()`, or `subsetVocabularyTables()` instead.

# View the updated concept entries for the 'Condition' domain
cdm$concept |> filter(domain_id == "Condition")
#> # A tibble: 21 × 10
#>    concept_id concept_name              domain_id vocabulary_id concept_class_id
#>         <int> <chr>                     <chr>     <chr>         <chr>           
#>  1     194152 Renal agenesis and dysge… Condition SNOMED        Clinical Finding
#>  2     444074 Victim of vehicular AND/… Condition SNOMED        Clinical Finding
#>  3    4151660 Alkaline phosphatase bon… Condition SNOMED        Clinical Finding
#>  4    4226696 Manic mood                Condition SNOMED        Clinical Finding
#>  5    4304866 Elevated mood             Condition SNOMED        Clinical Finding
#>  6   40475132 Arthropathies             Condition ICD10         ICD10 SubChapter
#>  7   40475135 Other joint disorders     Condition ICD10         ICD10 SubChapter
#>  8   45430573 Renal agenesis or dysgen… Condition Read          Read            
#>  9   45511667 Manic mood                Condition Read          Read            
#> 10   45533778 Other acquired deformiti… Condition ICD10         ICD10 Hierarchy 
#> # ℹ 11 more rows
#> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>