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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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75
tests/testthat/test-eucast_rules.R
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@@ -117,15 +117,16 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
}
# azithromycin and clarythromycin must be equal to Erythromycin
a <- suppressWarnings(as.sir(eucast_rules(data.frame(
mo = example_isolates$mo,
ERY = example_isolates$ERY,
AZM = as.sir("R"),
CLR = factor("R"),
stringsAsFactors = FALSE
),
version_expertrules = 3.1,
only_sir_columns = FALSE
a <- suppressWarnings(as.sir(eucast_rules(
data.frame(
mo = example_isolates$mo,
ERY = example_isolates$ERY,
AZM = as.sir("R"),
CLR = factor("R"),
stringsAsFactors = FALSE
),
version_expertrules = 3.1,
only_sir_columns = FALSE
)$CLR))
b <- example_isolates$ERY
expect_identical(
@@ -160,34 +161,37 @@ expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, ru
# AmpC de-repressed cephalo mutants
expect_identical(
eucast_rules(data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = TRUE,
info = FALSE
eucast_rules(
data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = TRUE,
info = FALSE
)$cefotax,
as.sir(c("S", "R"))
)
expect_identical(
eucast_rules(data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NA,
info = FALSE
eucast_rules(
data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NA,
info = FALSE
)$cefotax,
as.sir(c("S", NA))
)
expect_identical(
eucast_rules(data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NULL,
info = FALSE
eucast_rules(
data.frame(
mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NULL,
info = FALSE
)$cefotax,
as.sir(c("S", "S"))
)
@@ -208,12 +212,13 @@ expect_stdout(print(c(x, x)))
expect_stdout(print(as.list(x, x)))
# this custom rules makes 8 changes
expect_equal(nrow(eucast_rules(example_isolates,
rules = "custom",
custom_rules = x,
info = FALSE,
verbose = TRUE
)),
8,
tolerance = 0.5
expect_equal(
nrow(eucast_rules(example_isolates,
rules = "custom",
custom_rules = x,
info = FALSE,
verbose = TRUE
)),
8,
tolerance = 0.5
)