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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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26
inst/tinytest/test-first_isolate.R
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@ -52,8 +52,8 @@ expect_equal(
first_isolate(example_isolates,
col_mo = "mo",
col_date = "date",
col_patient_id = "patient_id",
col_icu = "ward_icu",
col_patient_id = "patient",
col_icu = example_isolates$ward == "ICU",
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
@ -67,7 +67,7 @@ x[random_rows, "specimen"] <- "Urine"
expect_true(
sum(first_isolate(x = x,
col_date = "date",
col_patient_id = "patient_id",
col_patient_id = "patient",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "Urine",
@ -76,11 +76,11 @@ expect_true(
expect_true(
sum(first_isolate(x = x,
col_date = "date",
col_patient_id = "patient_id",
col_patient_id = "patient",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "Urine",
col_icu = "ward_icu",
col_icu = x$ward == "ICU",
icu_exclude = TRUE,
info = TRUE), na.rm = TRUE) < 1501)
@ -89,7 +89,7 @@ test_iso <- example_isolates
test_iso$specimen <- "test"
expect_message(first_isolate(test_iso,
"date",
"patient_id",
"patient",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "something_unexisting",
@ -99,13 +99,13 @@ expect_message(first_isolate(test_iso,
expect_message(first_isolate(example_isolates,
col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_patient_id = "patient",
col_testcode = "gender",
testcodes_exclude = "M",
info = TRUE))
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate("date", "patient", col_mo = "mo"))
expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
@ -116,12 +116,12 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_patient_id = "patient",
info = FALSE),
example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_patient_id = "patient",
info = FALSE))
# support for WHONET
@ -133,8 +133,8 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
first_isolate(info = TRUE))
# groups
x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
x <- example_isolates %>% group_by(ward) %>% mutate(first = first_isolate())
y <- example_isolates %>% group_by(ward) %>% mutate(first = first_isolate(.))
expect_identical(x, y)
}
@ -146,7 +146,7 @@ expect_equal(
sum(
first_isolate(x = df,
col_date = "date",
col_patient_id = "patient_id",
col_patient_id = "patient",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),