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(v1.5.0.9007) updated unit tests

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dr. M.S. (Matthijs) Berends
2021-01-18 18:45:43 +01:00
parent 4eab095306
commit 27f084d819
17 changed files with 47 additions and 43 deletions
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13
tests/testthat/test-eucast_rules.R
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@@ -50,20 +50,21 @@ test_that("EUCAST rules work", {
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates))))
colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
@@ -81,8 +82,8 @@ test_that("EUCAST rules work", {
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
left_join_microorganisms() %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
left_join_microorganisms(by = "mo") %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
unique() %>%