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(v1.6.0.9000) custom EUCAST rules

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
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21
tests/testthat/test-eucast_rules.R
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@ -80,11 +80,10 @@ test_that("EUCAST rules work", {
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) %>%
left_join_microorganisms(by = "mo") %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
unique() %>%
as.character()),
@ -145,3 +144,21 @@ test_that("EUCAST rules work", {
expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
})
test_that("Custom EUCAST rules work", {
skip_on_cran()
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
expect_output(print(x))
expect_output(print(c(x, x)))
expect_output(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)
})