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(v2.1.1.9191) unit tests

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dr. M.S. (Matthijs) Berends
2025-03-10 12:16:45 +01:00
parent a2c2be23c1
commit 32024e597a
10 changed files with 37 additions and 22 deletions
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27
tests/testthat/test-antibiogram.R
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@ -31,18 +31,18 @@ test_that("antibiogram works", {
# Traditional antibiogram ----------------------------------------------
ab1 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems())
antimicrobials = c(aminoglycosides(), carbapenems())
)
ab2 <- antibiogram(example_isolates,
antibiotics = aminoglycosides(),
antimicrobials = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain",
add_total_n = TRUE
)
ab3 <- antibiogram(example_isolates,
antibiotics = carbapenems(),
antimicrobials = carbapenems(),
ab_transform = "ab",
mo_transform = "name",
formatting_type = 1
@ -58,14 +58,14 @@ test_that("antibiogram works", {
# Combined antibiogram -------------------------------------------------
# combined antibiotics yield higher empiric coverage
# combined antibiogram yield higher empiric coverage
ab4 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain"
)
ab5 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB"),
antimicrobials = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ",
@ -81,7 +81,7 @@ test_that("antibiogram works", {
# the data set could contain a filter for e.g. respiratory specimens
ab6 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
antimicrobials = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward",
ab_transform = NULL
)
@ -90,7 +90,7 @@ test_that("antibiogram works", {
# (i.e., this table will be in Dutch on Dutch systems)
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
ab7 <- antibiogram(ex1,
antibiotics = aminoglycosides(),
antimicrobials = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"IC", "Geen IC"
@ -108,7 +108,7 @@ test_that("antibiogram works", {
# the data set could contain a filter for e.g. respiratory specimens
ab8 <- suppressWarnings(antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
wisca = TRUE
))
@ -118,11 +118,12 @@ test_that("antibiogram works", {
expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
# grouped tibbles
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
ab9 <- example_isolates %>%
group_by(ward, gender) %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
expect_warning(
ab9 <- example_isolates %>%
group_by(ward, gender) %>%
wisca(antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
)
expect_equal(colnames(ab9), c("ward", "gender", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
}