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250 lines
7.8 KiB
R
250 lines
7.8 KiB
R
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# we must only have EUCAST and CLSI, because otherwise the rules in as.sir() will fail
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expect_identical(
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unique(gsub("[^A-Z]", "", AMR::clinical_breakpoints$guideline)),
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c("EUCAST", "CLSI")
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)
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expect_true(as.sir("S") < as.sir("I"))
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expect_true(as.sir("I") < as.sir("R"))
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expect_true(is.sir(as.sir("S")))
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x <- example_isolates$AMX
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expect_inherits(x[1], "sir")
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expect_inherits(x[[1]], "sir")
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expect_inherits(c(x[1], x[9]), "sir")
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expect_inherits(unique(x[1], x[9]), "sir")
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.sir(c("S", "I", "R"))))
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expect_silent(plot(as.sir(c("S", "I", "R"))))
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(ggplot2::autoplot(as.sir(c("S", "I", "R"))), "gg")
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}
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expect_stdout(print(as.sir(c("S", "I", "R"))))
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expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
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expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
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expect_equal(suppressWarnings(as.logical(as.sir("INVALID VALUE"))), NA)
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expect_equal(
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summary(as.sir(c("S", "R"))),
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structure(c(
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"Class" = "sir",
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"%R" = "50.0% (n=1)",
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"%SI" = "50.0% (n=1)",
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"- %S" = "50.0% (n=1)",
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"- %I" = " 0.0% (n=0)"
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), class = c("summaryDefault", "table"))
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)
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expect_identical(
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as.logical(lapply(example_isolates, is_sir_eligible)),
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as.logical(lapply(example_isolates, is.sir))
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)
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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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example_isolates %>%
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mutate_at(vars(PEN:RIF), as.character) %>%
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lapply(is_sir_eligible) %>%
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as.logical() %>%
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sum(),
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40
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)
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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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}
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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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skim(example_isolates),
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"data.frame"
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_inherits(
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example_isolates %>%
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mutate(
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m = as.mic(2),
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d = as.disk(20)
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) %>%
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skim(),
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"data.frame"
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)
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}
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}
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expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))
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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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)
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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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)
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)),
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c("S", "S", "I", "R", "R")
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)
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expect_true(is.data.frame(sir_interpretation_history(clean = FALSE)))
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expect_true(is.data.frame(sir_interpretation_history(clean = TRUE)))
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expect_true(is.null(sir_interpretation_history()))
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# cutoffs at MIC = 8
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expect_equal(
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suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
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as.sir("S")
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)
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expect_equal(
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suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
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as.sir("R")
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_true(suppressWarnings(example_isolates %>%
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mutate(amox_mic = as.mic(2)) %>%
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select(mo, amox_mic) %>%
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as.sir() %>%
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pull(amox_mic) %>%
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is.sir()))
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}
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expect_equal(
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as.character(
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as.sir(
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x = as.disk(22),
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mo = "B_STRPT_PNMN",
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ab = "ERY",
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guideline = "CLSI"
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)
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),
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"S"
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)
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expect_equal(
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as.character(
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as.sir(
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x = as.disk(18),
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mo = "B_STRPT_PNMN",
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ab = "ERY",
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guideline = "CLSI"
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)
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),
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"I"
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)
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expect_equal(
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as.character(
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as.sir(
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x = as.disk(10),
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mo = "B_STRPT_PNMN",
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ab = "ERY",
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guideline = "CLSI"
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)
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),
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"R"
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_true(example_isolates %>%
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mutate(amox_disk = as.disk(15)) %>%
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select(mo, amox_disk) %>%
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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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}
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# frequency tables
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if (AMR:::pkg_is_available("cleaner")) {
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expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
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}
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df <- data.frame(
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microorganism = "Escherichia coli",
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AMP = as.mic(8),
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CIP = as.mic(0.256),
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GEN = as.disk(18),
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TOB = as.disk(16),
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ERY = "R", # note about assigning <rsi> class
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CLR = "V"
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) # note about cleaning
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expect_inherits(
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suppressWarnings(as.sir(df)),
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"data.frame"
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)
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expect_inherits(
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suppressWarnings(as.sir(data.frame(
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mo = "Escherichia coli",
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amoxi = c("S", "I", "R", "invalid")
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))$amoxi),
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"sir"
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)
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# expect_warning(as.sir(data.frame(mo = "E. coli", NIT = c("<= 2", 32))))
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expect_message(as.sir(data.frame(
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mo = "E. coli",
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NIT = c("<= 2", 32),
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uti = TRUE
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)))
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expect_message(as.sir(data.frame(
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mo = "E. coli",
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NIT = c("<= 2", 32),
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specimen = c("urine", "blood")
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)))
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