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(v1.1.0.9021) 1st isolates update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
parent 86d44054f0
commit d9a4b0bcaf
51 changed files with 483 additions and 1106 deletions
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18
tests/testthat/test-first_isolate.R
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@ -34,7 +34,7 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1317)
1300)
# first weighted isolates
ex_iso_with_keyab <- example_isolates
@ -47,7 +47,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
1396)
# when not ignoring I
expect_equal(
@ -62,7 +62,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1436)
1419)
# when using points
expect_equal(
suppressWarnings(
@ -75,7 +75,7 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1417)
1400)
# first non-ICU isolates
expect_equal(
@ -88,7 +88,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
891)
881)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
@ -175,19 +175,19 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1322)
1305)
# unknown MOs
test_unknown <- example_isolates
test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)),
1062)
1045)
expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
1529)
1528)
test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown)),
1062)
1045)
# shortcuts
expect_identical(filter_first_isolate(example_isolates),