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

 # \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)
)
#> Warning: ! 5 casted column in person as do not match expected column type:
#> • `person_id` from numeric to integer
#> • `gender_concept_id` from numeric to integer
#> • `year_of_birth` from numeric to integer
#> • `race_concept_id` from numeric to integer
#> • `ethnicity_concept_id` from numeric to integer
#> Warning: ! 3 casted column in observation_period as do not match expected column type:
#> • `observation_period_id` from numeric to integer
#> • `person_id` from numeric to integer
#> • `period_type_concept_id` from numeric to integer
#> Warning: ! 2 casted column in cohort1 as do not match expected column type:
#> • `cohort_definition_id` from numeric to integer
#> • `subject_id` from numeric to integer
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")
#> 
#> ── 1 codelist ──────────────────────────────────────────────────────────────────
#> 
#> - disease X (3 codes)
# }