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(v2.1.1.9163) cleanup
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@ -88,18 +88,18 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_equal(sum(is.sir(example_isolates)), 40)
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expect_stdout(print(tibble(ab = as.sir("S"))))
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expect_true(example_isolates %>%
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select(AMC, MEM) %>%
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mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>%
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pull(MEM) %>%
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is.sir())
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expect_true(example_isolates %>%
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select(AMC, MEM) %>%
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mutate(MEM = if_else(AMC == "S", "S", MEM)) %>%
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pull(MEM) %>%
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is.sir())
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expect_true(example_isolates %>%
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select(AMC, MEM) %>%
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mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>%
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pull(MEM) %>%
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is.sir())
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expect_true(example_isolates %>%
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select(AMC, MEM) %>%
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mutate(MEM = if_else(AMC == "S", "S", MEM)) %>%
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pull(MEM) %>%
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is.sir())
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}
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if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
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expect_inherits(
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@ -124,58 +124,78 @@ expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir
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# Human -------------------------------------------------------------------
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mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
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expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
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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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expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
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uti = TRUE, include_PKPD = FALSE)),
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c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "R"))
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expect_identical(as.character(as.sir(mics, mo = "Escherichia coli", ab = "AMC", guideline = "EUCAST 2022",
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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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mics <- as.mic(2^c(-4:6)) # 0.0625 to 64 in factors of 2
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expect_identical(
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as.character(as.sir(mics,
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mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
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uti = FALSE, include_PKPD = FALSE
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)),
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c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R")
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)
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expect_identical(
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as.character(as.sir(mics,
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mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
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uti = TRUE, include_PKPD = FALSE
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)),
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c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "R")
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)
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expect_identical(
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as.character(as.sir(mics,
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mo = "Escherichia coli", ab = "AMC", guideline = "EUCAST 2022",
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uti = FALSE, include_PKPD = FALSE
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)),
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c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R")
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)
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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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out2 <- data.frame(
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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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) %>%
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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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out3 <- data.frame(
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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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) %>%
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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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as.character(
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as.sir(
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x = as.mic(c(0.125, 0.5, 1, 2, 4)),
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mo = "B_STRPT_PNMN",
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ab = "AMP",
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guideline = "EUCAST 2020"
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expect_equal(
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suppressMessages(
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as.character(
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as.sir(
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x = as.mic(c(0.125, 0.5, 1, 2, 4)),
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mo = "B_STRPT_PNMN",
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ab = "AMP",
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guideline = "EUCAST 2020"
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)
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)
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)),
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),
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c("S", "S", "I", "I", "R")
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)
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# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
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expect_equal(suppressMessages(
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as.character(
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as.sir(
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x = as.mic(c(1, 2, 4, 8, 16)),
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mo = "B_STRPT_PNMN",
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ab = "AMX",
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guideline = "CLSI 2019"
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expect_equal(
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suppressMessages(
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as.character(
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as.sir(
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x = as.mic(c(1, 2, 4, 8, 16)),
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mo = "B_STRPT_PNMN",
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ab = "AMX",
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guideline = "CLSI 2019"
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)
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)
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)),
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),
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c("S", "S", "I", "R", "R")
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)
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@ -241,20 +261,28 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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as.sir(guideline = "CLSI") %>%
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pull(amox_disk) %>%
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is.sir())
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# used by group_by() on sir_calc_df(), check some internals to see if grouped calculation without tidyverse works
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groups <- example_isolates %>%
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group_by(mo) %>%
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attributes() %>%
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.$groups
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expect_equal(nrow(groups),
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90)
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expect_equal(class(groups$.rows),
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c("vctrs_list_of", "vctrs_vctr", "list"))
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expect_equal(groups$.rows[[1]],
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c(101, 524, 1368))
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expect_equal(example_isolates[c(101, 524, 1368), "mo", drop = TRUE],
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rep(groups$mo[1], 3))
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expect_equal(
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nrow(groups),
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90
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)
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expect_equal(
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class(groups$.rows),
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c("vctrs_list_of", "vctrs_vctr", "list")
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)
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expect_equal(
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groups$.rows[[1]],
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c(101, 524, 1368)
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)
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expect_equal(
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example_isolates[c(101, 524, 1368), "mo", drop = TRUE],
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rep(groups$mo[1], 3)
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)
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}
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# frequency tables
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if (AMR:::pkg_is_available("cleaner")) {
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@ -295,27 +323,35 @@ expect_message(as.sir(data.frame(
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)))
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# SDD vs I in CLSI 2024
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expect_identical(as.sir(as.mic(2 ^ c(-2:4)), mo = "Enterococcus faecium", ab = "Dapto", guideline = "CLSI 2024"),
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as.sir(c("SDD", "SDD", "SDD", "SDD", "SDD", "R", "R")))
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expect_identical(as.sir(as.mic(2 ^ c(-2:2)), mo = "Enterococcus faecium", ab = "Cipro
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expect_identical(
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as.sir(as.mic(2^c(-2:4)), mo = "Enterococcus faecium", ab = "Dapto", guideline = "CLSI 2024"),
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as.sir(c("SDD", "SDD", "SDD", "SDD", "SDD", "R", "R"))
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)
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expect_identical(
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as.sir(as.mic(2^c(-2:2)), mo = "Enterococcus faecium", ab = "Cipro
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", guideline = "CLSI 2024"),
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as.sir(c("S", "S", "S", "I", "R")))
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as.sir(c("S", "S", "S", "I", "R"))
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)
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# Veterinary --------------------------------------------------------------
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sir_history <- sir_interpretation_history(clean = TRUE)
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mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
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vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
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PRA = mics,
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FLR = mics,
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mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
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mics <- as.mic(2^c(-4:6)) # 0.0625 to 64 in factors of 2
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vet <- data.frame(
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animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
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PRA = mics,
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FLR = mics,
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mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1])
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)
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out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
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# host column name instead of values
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expect_identical(out_vet,
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as.sir(vet, host = "animal", guideline = "CLSI 2023"))
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expect_identical(
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out_vet,
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as.sir(vet, host = "animal", guideline = "CLSI 2023")
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)
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# check outcomes
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expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
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@ -326,11 +362,15 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11))
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expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
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sir_history <- sir_interpretation_history()
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expect_identical(sort(sir_history$host),
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c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
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"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
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"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
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"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry","poultry","poultry","poultry"))
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expect_identical(
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sort(sir_history$host),
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c(
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"cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
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"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
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"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
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"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry", "poultry", "poultry", "poultry"
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)
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)
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# ECOFF -------------------------------------------------------------------
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@ -340,4 +380,3 @@ expect_equal(
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)
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# old method
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expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
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