Merge pull request #359 from OHDSI/max_age_inf

allow max age to be Inf

R/requireDemographics.R

@@ -610,10 +610,11 @@ reqDemographicsCohortSet <- function(set,
  .data$cohort_name
  ))
  }
-
  combinations <- combinations |>
- dplyr::mutate(min_age = as.integer(sub("_.*", "", .data$age_range)), max_age = as.integer(sub(".*_", "", .data$age_range))) |>
- dplyr::mutate(age_range = stringr::str_replace(.data$age_range, "_999", "_Inf")) |>
+ dplyr::mutate(min_age = as.integer(sub("_.*", "", .data$age_range)),
+ max_age = sub(".*_", "", .data$age_range)) |>
+ dplyr::mutate(max_age = stringr::str_replace(.data$max_age, "Inf", "999")) |>
+ dplyr::mutate(max_age = as.integer(.data$max_age)) |>
  dplyr::select(!c("group_id"))
 
  # new cohort set

R/trimDemographics.R

@@ -42,10 +42,6 @@ trimDemographics <- function(cohort,
  ids <- settings(cohort)$cohort_definition_id
 
  # replace age Inf to avoid potential sql issues
- for (j in seq_along(ageRange)) {
- ageRange[[j]][is.infinite(ageRange[[j]])] <- as.integer(999)
- }
-
  # temp tables
  tablePrefix <- omopgenerics::tmpPrefix()
  tmpName <- omopgenerics::uniqueTableName(tablePrefix)
@@ -91,6 +87,7 @@ trimDemographics <- function(cohort,
  minFutureObservation = minFutureObservation,
  requirementInteractions = TRUE
  )
+
  # insert settings
  cdm <- omopgenerics::insertTable(
  cdm = cdm,
@@ -152,6 +149,11 @@ trimDemographics <- function(cohort,
  }
  if (!is.null(ageRange)) {
  cli::cli_inform(c("Trim age"))
+
+ for (j in seq_along(ageRange)) {
+ ageRange[[j]][is.infinite(ageRange[[j]])] <- as.integer(999)
+ }
+
  newCohort <- newCohort %>%
  dplyr::mutate(!!!datesAgeRange(ageRange)) %>%
  dplyr::mutate(

tests/testthat/test-requireDemographics.R

@@ -521,3 +521,25 @@ test_that("requireInteractions", {
  )
  PatientProfiles::mockDisconnect(cdm)
 })
+
+test_that("Inf age", {
+
+ testthat::skip_on_cran()
+ cdm_local <- omock::mockCdmReference() |>
+ omock::mockPerson(n = 3,seed = 1) |>
+ omock::mockObservationPeriod(seed = 1) |>
+ omock::mockCohort(numberCohorts = 3, seed = 4)
+ # to remove in new omock
+ cdm_local$person <- cdm_local$person |>
+ dplyr::mutate(dplyr::across(dplyr::ends_with("of_birth"), ~ as.numeric(.x)))
+ cdm <- cdm_local |> copyCdm()
+
+ expect_no_error(cdm$cohort1 <- cdm$cohort |>
+ requireDemographics(ageRange = c(0, Inf),
+ name = "cohort1"))
+ expect_no_error(cdm$cohort2 <-cdm$cohort |>
+ requireDemographics(ageRange = list(c(0, 17),
+ c(18,Inf)),
+ name = "cohort2"))
+
+})