omopgenerics (version 1.3.2)

cohortCodelist: 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()
)

Value

A table with the codelists used.

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.

Examples

 # \donttest{
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")
# }