date transformation fix for tibbles

R/first_isolate.R

@@ -172,8 +172,8 @@ first_isolate <- function(tbl,
   if (is.null(col_date)) {
     stop("`col_date` must be set.", call. = FALSE)
   }
-  # convert to Date
-  tbl[, col_date] <- as.Date(tbl[, col_date])
+  # convert to Date (pipes for supporting tibbles too)
+  tbl[, col_date] <- tbl %>% pull(col_date) %>% as.Date()
 
   # -- patient id
   if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) {

tests/testthat/test-first_isolate.R

@@ -26,6 +26,20 @@ test_that("first isolates work", {
                       info = TRUE),
         na.rm = TRUE)),
     1411)
+  # should be same for tibbles
+  expect_equal(
+    suppressWarnings(
+      sum(
+        first_isolate(tbl = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
+                      # let syntax determine these automatically:
+                      # col_date = "date",
+                      # col_patient_id = "patient_id",
+                      # col_mo = "mo",
+                      # col_keyantibiotics = "keyab",
+                      type = "keyantibiotics",
+                      info = TRUE),
+        na.rm = TRUE)),
+    1411)
   # and 1435 when not ignoring I
   expect_equal(
     suppressWarnings(