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(v1.6.0.9022) unit test fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-13 15:56:12 +02:00
parent 29dbfa2f49
commit 655b813e99
19 changed files with 84 additions and 61 deletions
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27
tests/testthat/test-eucast_rules.R
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@ -77,17 +77,18 @@ test_that("EUCAST rules work", {
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr, warn.conflicts = FALSE)
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
pull(PIP) %>%
unique() %>%
as.character()),
"R")
if (require("dplyr")) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
pull(PIP) %>%
unique() %>%
as.character()),
"R")
}
# Azithromycin and Clarythromycin must be equal to Erythromycin
a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
@ -114,7 +115,9 @@ test_that("EUCAST rules work", {
"S")
# also test norf
expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
if (require("dplyr")) {
expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}
# check verbose output
expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))