Set cohort end date to the last of a set of column dates
exitAtLastDate.Rd
exitAtLastDate()
resets cohort end date based on a set of specified
column dates. The last date that occurs is chosen.
Usage
exitAtLastDate(
cohort,
dateColumns,
cohortId = NULL,
returnReason = TRUE,
name = tableName(cohort)
)
Arguments
- cohort
A cohort table in a cdm reference.
- dateColumns
Character vector indicating date columns in the cohort table to consider.
- cohortId
Vector identifying which cohorts to modify (cohort_definition_id or cohort_name). If NULL, all cohorts will be used; otherwise, only the specified cohorts will be modified, and the rest will remain unchanged.
- returnReason
If TRUE it will return a column indicating which of the
dateColumns
was used.- name
Name of the new cohort table created in the cdm object.
Examples
# \donttest{
library(CohortConstructor)
cdm <- mockCohortConstructor(tables = list(
"cohort" = dplyr::tibble(
cohort_definition_id = 1,
subject_id = c(1, 2, 3, 4),
cohort_start_date = as.Date(c("2000-06-03", "2000-01-01", "2015-01-15", "2000-12-09")),
cohort_end_date = as.Date(c("2001-09-01", "2001-01-12", "2015-02-15", "2002-12-09")),
date_1 = as.Date(c("2001-08-01", "2001-01-01", "2015-01-15", "2002-12-09")),
date_2 = as.Date(c("2001-08-01", NA, "2015-04-15", "2002-12-09"))
)
))
#> Warning: ! 7 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `month_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> • `location_id` is numeric but expected integer
#> Warning: ! 2 column in observation_period do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: ! 9 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `cdm_version` is numeric but expected character
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: ! 1 column in vocabulary do not match expected column type:
#> • `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 5 column in concept_relationship do not match expected column type:
#> • `concept_id_1` is numeric but expected integer
#> • `concept_id_2` is numeric but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 2 column in concept_synonym do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `language_concept_id` is numeric but expected integer
#> Warning: ! 4 column in concept_ancestor do not match expected column type:
#> • `ancestor_concept_id` is numeric but expected integer
#> • `descendant_concept_id` is numeric but expected integer
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 9 column in drug_strength do not match expected column type:
#> • `drug_concept_id` is numeric but expected integer
#> • `ingredient_concept_id` is numeric but expected integer
#> • `amount_value` is logical but expected numeric
#> • `amount_unit_concept_id` is numeric but expected integer
#> • `numerator_unit_concept_id` is numeric but expected integer
#> • `denominator_unit_concept_id` is numeric but expected integer
#> • `box_size` is logical but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> Warning: ! 2 column in cohort do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> • `subject_id` is numeric but expected integer
#> Warning: ! 2 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `location_id` is numeric but expected integer
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `person_id` is numeric but expected integer
#> Warning: ! 2 column in cohort do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> • `subject_id` is numeric but expected integer
cdm$cohort |> exitAtLastDate(dateColumns = c("date_1", "date_2"))
#> Warning: ! 2 column in cohort do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> • `subject_id` is numeric but expected integer
#> # Source: table<main.cohort> [4 x 5]
#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason
#> <dbl> <dbl> <date> <date> <chr>
#> 1 1 2 2000-01-01 2001-01-01 date_1
#> 2 1 1 2000-06-03 2001-08-01 date_1; dat…
#> 3 1 4 2000-12-09 2002-12-09 date_1; dat…
#> 4 1 3 2015-01-15 2015-04-15 date_2
# }