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fortify code with more tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-04-03 11:08:31 +02:00
parent 972e923484
commit 4a47e59e6f
4 changed files with 89 additions and 28 deletions
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26
tests/testthat/test-first_isolates.R
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@@ -14,18 +14,18 @@ test_that("guess_bactid works", {
test_that("first isolates work", {
# septic_patients contains 1960 out of 2000 first isolates
septic_ptns <- septic_patients
expect_equal(sum(first_isolate(tbl = septic_ptns,
#septic_ptns <- septic_patients
expect_equal(sum(first_isolate(tbl = septic_patients,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE)), 1960)
# septic_patients contains 1962 out of 2000 first weighted isolates
septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
# septic_patients contains 1962 out of 2000 first *weighted* isolates
#septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
expect_equal(
suppressWarnings(sum(
first_isolate(tbl = septic_ptns,
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
@@ -33,4 +33,20 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE))),
1962)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
expect_lt(sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_specimen = "specimen",
filter_specimen = "Urine",
info = TRUE)),
1501)
})