Adds the cohort_codelist attribute to a cohort

addCodelistAttribute() allows the users to add a codelist to a cohort in OMOP CDM.

This is particularly important for the use of codelistDiagnostics(), as the underlying assumption is that the cohort that is fed into codelistDiagnostics() has a cohort_codelist attribute attached to it.

Usage

addCodelistAttribute(cohort, codelist, cohortName = names(codelist))

Arguments

cohort

Cohort table in a cdm reference

codelist

Named list of concepts

cohortName

For each element of the codelist, the name of the cohort in cohort to which the codelist refers

Value

A cohort

Examples

# \donttest{
library(omock)
library(CohortConstructor)
library(PhenotypeR)

cdm <- mockCdmFromDataset(source = "duckdb")
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmprdhPUv/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
cdm$warfarin <- conceptCohort(cdm,
                              conceptSet =  list(warfarin = c(1310149L,
                                                              40163554L)),
                              name = "warfarin")
#> ℹ Subsetting table drug_exposure using 2 concepts with domain: drug.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort warfarin created.

cohort <- addCodelistAttribute(cohort = cdm$warfarin,
               codelist = list("warfarin" = c(1310149L,  40163554L)))
#> Warning: Overwriting codelist for cohort warfarin
attr(cohort, "cohort_codelist")
#> # A query:  ?? x 4
#> # Database: DuckDB 1.5.5 [unknown@Linux 6.17.0-1020-azure:R 4.6.1//tmp/RtmprdhPUv/file1c826f127199.duckdb]
#>   cohort_definition_id codelist_name concept_id codelist_type
#>                  <int> <chr>              <int> <chr>        
#> 1                    1 warfarin         1310149 index event  
#> 2                    1 warfarin        40163554 index event  

CDMConnector::cdmDisconnect(cdm)
# }