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fix SIR interpretation
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@ -71,6 +71,7 @@ expect_identical(
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expect_error(as.sir.mic(as.mic(16)))
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expect_error(as.sir.disk(as.disk(16)))
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expect_error(get_guideline("this one does not exist"))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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# 40 sir columns
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expect_equal(
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@ -125,6 +126,24 @@ expect_identical(as.character(as.sir(mics, mo = "Escherichia coli", ab = "AMC",
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uti = FALSE, include_PKPD = FALSE)),
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c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R"))
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# test SIR using dplyr's mutate_if(...) and mutate(across(...))
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out1 <- as.sir(as.mic(c(0.256, 0.5, 1, 2)), mo = "Escherichia coli", ab = "ertapenem", guideline = "EUCAST 2023")
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expect_identical(out1, as.sir(c("S", "S", "R", "R")))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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out2 <- data.frame(mo = "Escherichia coli",
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ab = "ertapenem",
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some_mics = as.mic(c(0.256, 0.5, 1, 2))) |>
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mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) |>
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pull(some_mics)
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out3 <- data.frame(mo = "Escherichia coli",
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ab = "ertapenem",
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some_mics = as.mic(c(0.256, 0.5, 1, 2))) |>
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mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") |>
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pull(some_mics)
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expect_identical(out1, out2)
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expect_identical(out1, out3)
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}
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# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
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expect_equal(suppressMessages(
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