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date transformation fix for tibbles
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@ -172,8 +172,8 @@ first_isolate <- function(tbl,
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if (is.null(col_date)) {
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stop("`col_date` must be set.", call. = FALSE)
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}
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# convert to Date
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tbl[, col_date] <- as.Date(tbl[, col_date])
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# convert to Date (pipes for supporting tibbles too)
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tbl[, col_date] <- tbl %>% pull(col_date) %>% as.Date()
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# -- patient id
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if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) {
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@ -26,6 +26,20 @@ test_that("first isolates work", {
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info = TRUE),
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na.rm = TRUE)),
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1411)
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# should be same for tibbles
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(tbl = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
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# let syntax determine these automatically:
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# col_date = "date",
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# col_patient_id = "patient_id",
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# col_mo = "mo",
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# col_keyantibiotics = "keyab",
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1411)
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# and 1435 when not ignoring I
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expect_equal(
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suppressWarnings(
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