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(v0.6.1.9044) first_isolate fix for species

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-31 14:25:11 +02:00
parent 1f8ee3ec3e
commit 493ae2ba0c
121 changed files with 586 additions and 521 deletions
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6
tests/testthat/test-age.R
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@ -26,6 +26,12 @@ test_that("age works", {
reference = "2019-01-01"),
c(39, 34, 29))
expect_equal(age(x = c("2019-01-01", "2019-04-01", "2019-07-01"),
reference = "2019-09-01",
exact = TRUE),
c(0.6656393, 0.4191781, 0.1698630),
tolerance = 0.000001)
expect_error(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
reference = c("2019-01-01", "2019-01-01")))

15
tests/testthat/test-first_isolate.R
View File

@ -31,7 +31,7 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1274)
1317)
# first *weighted* isolates
expect_equal(
@ -46,7 +46,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1369)
1413)
# should be same for tibbles
expect_equal(
suppressWarnings(
@ -60,7 +60,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1369)
1413)
# when not ignoring I
expect_equal(
suppressWarnings(
@ -74,7 +74,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1392)
1436)
# when using points
expect_equal(
suppressWarnings(
@ -87,7 +87,7 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1372)
1417)
# first non-ICU isolates
expect_equal(
@ -100,7 +100,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1129)
1163)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
@ -175,6 +175,7 @@ test_that("first isolates work", {
col_mo = "mo",
col_patient_id = "patient_id"))
# missing dates should be no problem
df <- septic_patients
df[1:100, "date"] <- NA
expect_equal(
@ -185,6 +186,6 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1279)
1322)
})