Create the obesity cohort

Usage

obesityCohort(cdm, name, conceptSet = NULL, bmiThreshold = NULL)

Arguments

cdm

A <cdm_reference> object.

name

A character string with the name of the new cohort.

conceptSet

It can either be a , <codelist_with_details> or <concept_set_expression> object. It must contain obesity, bmi as concepts. If NULL concepts will be retrieved using the OmopConcepts package.

bmiThreshold

Argument to indicate the thresholds for the obesity using BMI measurements. It can be:

A single number, any BMI measurement above the threshold will be consider as an obesity record.
A tibble with the columns bmi_threshold, sex, age_min and age_max, to use age and sex specific thresholds.
NULL the table CohortRecipes::bmiThreshold will be used.

Value

The cohort 'obesity' object.

Examples

# \donttest{
library(CohortRecipes)
library(omock)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", 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.

cdm$obesity <- obesityCohort(cdm = cdm, name = "obesity")
#> ! `conceptSet` is `NULL`, the conceptSet will be downloaded using OmopConcepts
#> ℹ Set `options('omop.concepts.source' = 'OmopConcepts')` to silence this
#>   message.
#> ℹ Using internal bmiThreshold for BMI cut-offs.
#> ✖ Domain NA (85 concepts) excluded because it is not supported.
#> ℹ No cohort entries found, returning empty cohort table.

cdm$obesity
#> # Source:   table<results.test_obesity> [?? x 4]
#> # Database: DuckDB 1.5.2 [unknown@Linux 6.17.0-1010-azure:R 4.5.3//tmp/Rtmpwzbprc/file1b1f6371b99a.duckdb]
#> # ℹ 4 variables: cohort_definition_id <int>, subject_id <int>,
#> #   cohort_start_date <date>, cohort_end_date <date>

# }