cohortCodelist: Get codelist from a cohort_table object.

In omopgenerics: Methods and Classes for the OMOP Common Data Model

Get codelist from a cohort_table object.

Description

Get codelist from a cohort_table object.

Usage

cohortCodelist(
  cohort,
  cohortId = NULL,
  codelistType = c("index event", "inclusion criteria", "exit criteria"),
  type = lifecycle::deprecated(),
  cohortTable = lifecycle::deprecated()
)

Arguments

cohort	A cohort_table object.
cohortId	A particular cohort definition id that is present in the cohort table. If NULL the codelists of all cohorts will be retrieved.
codelistType	The reason for the codelist. Can be "index event", "inclusion criteria", or "exit criteria".
type	deprecated.
cohortTable	deprecated.

Value

A table with the codelists used.

Examples

 
library(omopgenerics)
library(dplyr, warn.conflicts = FALSE)

person <- tibble(
  person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
  race_concept_id = 0, ethnicity_concept_id = 0
)
observation_period <- tibble(
  observation_period_id = 1, person_id = 1,
  observation_period_start_date = as.Date("2000-01-01"),
  observation_period_end_date = as.Date("2023-12-31"),
  period_type_concept_id = 0
)
cohort <- tibble(
  cohort_definition_id = c(1, 1, 1, 2),
  subject_id = 1,
  cohort_start_date = as.Date(c(
    "2020-01-01", "2021-01-01", "2022-01-01", "2022-01-01"
  )),
  cohort_end_date = as.Date(c(
    "2020-01-01", "2021-01-01", "2022-01-01", "2022-01-01"
  ))
)
cdm <- cdmFromTables(
  tables = list("person" = person, "observation_period" = observation_period),
  cdmName = "my_example_cdm",
  cohortTables = list("cohort1" = cohort)
)
cdm$cohort1 <- newCohortTable(table = cdm$cohort1,
                                cohortCodelistRef = dplyr::tibble(
                                cohort_definition_id = c(1,1,1,2,2),
                                codelist_name =c("disease X", "disease X", "disease X",
                                                 "disease Y", "disease Y"),
                                concept_id = c(1,2,3,4,5),
                                codelist_type = "index event"
                              ))
cohortCodelist(cdm$cohort1, cohortId = 1, codelistType = "index event")

omopgenerics documentation built on Dec. 1, 2025, 5:07 p.m.