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(v0.7.1.9063) septic_patients -> example_isolates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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38
tests/testthat/test-first_isolate.R
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@ -25,7 +25,7 @@ test_that("first isolates work", {
# first isolates
expect_equal(
sum(
first_isolate(x = septic_patients,
first_isolate(x = example_isolates,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -37,7 +37,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -51,7 +51,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -65,7 +65,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -79,7 +79,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -92,7 +92,7 @@ test_that("first isolates work", {
# first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
first_isolate(example_isolates,
col_mo = "mo",
col_date = "date",
col_patient_id = "patient_id",
@ -106,7 +106,7 @@ test_that("first isolates work", {
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
expect_lt(
sum(
first_isolate(x = mutate(septic_patients,
first_isolate(x = mutate(example_isolates,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -121,7 +121,7 @@ test_that("first isolates work", {
# same, but now exclude ICU
expect_lt(
sum(
first_isolate(x = mutate(septic_patients,
first_isolate(x = mutate(example_isolates,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -137,7 +137,7 @@ test_that("first isolates work", {
1501)
# "No isolates found"
expect_message(septic_patients %>%
expect_message(example_isolates %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
col_mo = "mo",
@ -145,7 +145,7 @@ test_that("first isolates work", {
filter_specimen = "something_unexisting")))
# printing of exclusion message
expect_output(septic_patients %>%
expect_output(example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
@ -154,29 +154,29 @@ test_that("first isolates work", {
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(septic_patients,
expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
# look for columns itself
expect_message(first_isolate(septic_patients))
expect_message(first_isolate(septic_patients %>%
expect_message(first_isolate(example_isolates))
expect_message(first_isolate(example_isolates %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms()))
# if mo is not an mo class, result should be the same
expect_identical(septic_patients %>%
expect_identical(example_isolates %>%
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
septic_patients %>%
example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"))
# missing dates should be no problem
df <- septic_patients
df <- example_isolates
df[1:100, "date"] <- NA
expect_equal(
sum(
@ -189,19 +189,19 @@ test_that("first isolates work", {
1322)
# unknown MOs
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = FALSE)) %>%
.$first %>%
sum(),
1062)
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = TRUE)) %>%
.$first %>%
sum(),
1529)
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", NA, mo)) %>%
mutate(first = first_isolate(.)) %>%
.$first %>%