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ggplot_rsi example update, more unit tests

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dr. M.S. (Matthijs) Berends
2018-08-29 16:25:57 +02:00
parent 029157b3be
commit d9e68e0a50
10 changed files with 121 additions and 18 deletions
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42
tests/testthat/test-first_isolate.R
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@ -25,6 +25,20 @@ test_that("first isolates work", {
info = TRUE),
na.rm = TRUE)),
1426)
# and 1449 when not ignoring I
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
ignore_I = FALSE,
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1449)
# and 1430 when using points
expect_equal(
suppressWarnings(
@ -86,10 +100,34 @@ test_that("first isolates work", {
na.rm = TRUE),
1501)
# "No isolates found"
expect_message(septic_patients %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
col_bactid = "bactid", col_specimen = "specimen",
filter_specimen = "something_unexisting")))
col_bactid = "bactid",
col_specimen = "specimen",
filter_specimen = "something_unexisting",
output_logical = FALSE)))
# printing of exclusion message
expect_output(septic_patients %>%
first_isolate(col_date = "date",
col_bactid = "bactid",
col_patient_id = "patient_id",
col_testcode = "sex",
testcodes_exclude = "M"))
# errors
expect_error(first_isolate("date", "patient_id", col_bactid = "bactid"))
expect_error(first_isolate(septic_patients))
expect_error(first_isolate(septic_patients,
col_date = "non-existing col",
col_bactid = "bactid"))
expect_warning(septic_patients %>%
mutate(bactid = as.character(bactid)) %>%
first_isolate(col_date = "date",
col_bactid = "bactid",
col_patient_id = "patient_id"))
})