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(v1.6.0.9065) unit tests

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dr. M.S. (Matthijs) Berends
2021-05-24 11:01:32 +02:00
parent 4fbf9e1720
commit e5599bc694
22 changed files with 126 additions and 133 deletions
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6
inst/tinytest/test-eucast_rules.R
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@ -45,6 +45,7 @@ expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S"
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
expect_stdout(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
a <- data.frame(mo = c("Klebsiella pneumoniae",
@ -84,7 +85,7 @@ if (AMR:::pkg_is_available("dplyr")) {
"R")
}
# Azithromycin and Clarythromycin must be equal to Erythromycin
# azithromycin and clarythromycin must be equal to Erythromycin
a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
ERY = example_isolates$ERY,
AZM = as.rsi("R"),
@ -117,18 +118,21 @@ if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
# AmpC de-repressed cephalo mutants
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = TRUE,
info = FALSE)$cefotax,
as.rsi(c("S", "R")))
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = NA,
info = FALSE)$cefotax,
as.rsi(c("S", NA)))
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),