fixes cast omop columns as omopgenerics specifies #103

#103
OHDSI · Aug 22, 2024 · 57e10c3 · 57e10c3
1 parent f7ed1d0
commit 57e10c3
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/R/mockObservationPeriod.R b/R/mockObservationPeriod.R
@@ -73,7 +73,7 @@ mockObservationPeriod <- function(cdm,
     )
 
     observationPeriod <-
-      observationPeriod |> dplyr::mutate(period_type_concept_id = NA)
+      observationPeriod |> dplyr::mutate(period_type_concept_id = as.integer(NA))
 
     cdm <-
       omopgenerics::insertTable(

diff --git a/R/mockPerson.R b/R/mockPerson.R
@@ -76,15 +76,15 @@ mockPerson <- function(cdm = mockCdmReference(),
 
     person <- dplyr::tibble(
       person_id = person_id,
-      gender_concept_id = gender,
-      year_of_birth = as.numeric(lubridate::year(dob)),
-      month_of_birth = as.numeric(lubridate::month(dob)),
-      day_of_birth = as.numeric(lubridate::day(dob))
+      gender_concept_id = as.integer(gender),
+      year_of_birth = as.integer(lubridate::year(dob)),
+      month_of_birth = as.integer(lubridate::month(dob)),
+      day_of_birth = as.integer(lubridate::day(dob))
     )
     person <- person |>
       dplyr::mutate(
-        race_concept_id = NA,
-        ethnicity_concept_id = NA
+        race_concept_id = as.integer(NA),
+        ethnicity_concept_id = as.integer(NA)
       )
 
 

diff --git a/R/mockVisitOccurrence.R b/R/mockVisitOccurrence.R
@@ -31,8 +31,8 @@ mockVisitOccurrence <- function(cdm,
   }
 
   # check if table are empty
-  if (cdm$person |> nrow() == 0 |
-    cdm$observation_period |> nrow() == 0 | is.null(cdm$concept)) {
+  if (cdm$person |> nrow() == 0 ||
+      cdm$observation_period |> nrow() == 0 || is.null(cdm$concept)) {
     cli::cli_abort("person and observation_period table cannot be empty")
   }