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(v1.6.0.9065) unit tests

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This commit is contained in:
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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24
inst/tinytest/test-_misc.R
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@ -22,34 +22,32 @@
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(AMR:::percentage(0.25), "25%")
expect_equal(AMR:::percentage(0.5), "50%")
expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%")
expect_equal(AMR:::percentage(0.1234), "12.3%")
# round up 0.5
# round up 0.5
expect_equal(AMR:::percentage(0.0054), "0.5%")
expect_equal(AMR:::percentage(0.0055), "0.6%")
expect_equal(AMR:::strrep("A", 5), "AAAAA")
expect_equal(AMR:::strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
expect_equal(AMR:::trimws(" test "), "test")
expect_equal(AMR:::trimws(" test ", "l"), "test ")
expect_equal(AMR:::trimws(" test ", "r"), " test")
expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
if (AMR:::pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
if (AMR:::pkg_is_available("dplyr")) {
expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}
}
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
if (AMR:::pkg_is_available("dplyr")) {
expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}

4
inst/tinytest/test-count.R
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@ -36,11 +36,9 @@ expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
count_SI(example_isolates$AMX))
# warning for speed loss
AMR:::reset_all_thrown_messages()
expect_warning(count_resistant(as.character(example_isolates$AMC)))
AMR:::reset_all_thrown_messages()
expect_warning(count_resistant(example_isolates$AMC,
as.character(example_isolates$GEN)))

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"))),

9
inst/tinytest/test-proportion.R
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@ -88,14 +88,12 @@ if (AMR:::pkg_is_available("dplyr")) {
example_isolates$AMX %>% proportion_R())
)
}
AMR:::reset_all_thrown_messages()
expect_warning(proportion_R(as.character(example_isolates$AMC)))
AMR:::reset_all_thrown_messages()
expect_warning(proportion_S(as.character(example_isolates$AMC)))
AMR:::reset_all_thrown_messages()
expect_warning(proportion_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
AMR:::reset_all_thrown_messages()
expect_warning(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
@ -120,11 +118,8 @@ expect_identical(suppressWarnings(proportion_S(example_isolates$AMX, minimum = n
NA_real_)
# warning for speed loss
AMR:::reset_all_thrown_messages()
expect_warning(proportion_R(as.character(example_isolates$GEN)))
AMR:::reset_all_thrown_messages()
expect_warning(proportion_I(as.character(example_isolates$GEN)))
AMR:::reset_all_thrown_messages()
expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
expect_error(proportion_df(c("A", "B", "C")))
expect_error(proportion_df(example_isolates[, "date"]))