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fix SIR interpretation

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-05-31 09:50:54 +02:00
parent ba4dc20cf3
commit 60c6c21e45
6 changed files with 128 additions and 66 deletions
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19
inst/tinytest/test-sir.R
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@ -71,6 +71,7 @@ expect_identical(
expect_error(as.sir.mic(as.mic(16)))
expect_error(as.sir.disk(as.disk(16)))
expect_error(get_guideline("this one does not exist"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
# 40 sir columns
expect_equal(
@ -125,6 +126,24 @@ expect_identical(as.character(as.sir(mics, mo = "Escherichia coli", ab = "AMC",
uti = FALSE, include_PKPD = FALSE)),
c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R"))
# test SIR using dplyr's mutate_if(...) and mutate(across(...))
out1 <- as.sir(as.mic(c(0.256, 0.5, 1, 2)), mo = "Escherichia coli", ab = "ertapenem", guideline = "EUCAST 2023")
expect_identical(out1, as.sir(c("S", "S", "R", "R")))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
out2 <- data.frame(mo = "Escherichia coli",
ab = "ertapenem",
some_mics = as.mic(c(0.256, 0.5, 1, 2))) |>
mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) |>
pull(some_mics)
out3 <- data.frame(mo = "Escherichia coli",
ab = "ertapenem",
some_mics = as.mic(c(0.256, 0.5, 1, 2))) |>
mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") |>
pull(some_mics)
expect_identical(out1, out2)
expect_identical(out1, out3)
}
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(suppressMessages(