mirror of https://github.com/msberends/AMR.git
158 lines
6.6 KiB
R
158 lines
6.6 KiB
R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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expect_true(as.rsi("S") < as.rsi("I"))
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expect_true(as.rsi("I") < as.rsi("R"))
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expect_true(is.rsi(as.rsi("S")))
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x <- example_isolates$AMX
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expect_inherits(x[1], "rsi")
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expect_inherits(x[[1]], "rsi")
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expect_inherits(c(x[1], x[9]), "rsi")
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expect_inherits(unique(x[1], x[9]), "rsi")
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.rsi(c("S", "I", "R"))))
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expect_silent(plot(as.rsi(c("S", "I", "R"))))
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if (suppressWarnings(require("ggplot2"))) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
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expect_stdout(print(as.rsi(c("S", "I", "R"))))
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expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
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expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
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expect_equal(summary(as.rsi(c("S", "R"))),
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structure(c("Class" = "rsi",
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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)"), class = c("summaryDefault", "table")))
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expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
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rep(FALSE, length(example_isolates)))
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expect_error(as.rsi.mic(as.mic(16)))
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expect_error(as.rsi.disk(as.disk(16)))
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expect_error(get_guideline("this one does not exist"))
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if (suppressWarnings(require("dplyr"))) {
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# 40 rsi columns
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expect_equal(example_isolates %>%
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mutate_at(vars(PEN:RIF), as.character) %>%
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lapply(is.rsi.eligible) %>%
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as.logical() %>%
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sum(),
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40)
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expect_equal(sum(is.rsi(example_isolates)), 40)
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expect_stdout(print(tibble(ab = as.rsi("S"))))
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}
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if (suppressWarnings(require("skimr"))) {
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expect_inherits(skim(example_isolates),
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"data.frame")
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if (suppressWarnings(require("dplyr"))) {
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expect_inherits(example_isolates %>%
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mutate(m = as.mic(2),
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d = as.disk(20)) %>%
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skim(),
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"data.frame")
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}
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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(as.character(
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as.rsi(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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c("S", "S", "I", "I", "R"))
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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(as.character(
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as.rsi(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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c("S", "S", "I", "R", "R"))
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# cutoffs at MIC = 8
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expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
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as.rsi("S"))
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expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
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as.rsi("R"))
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if (suppressWarnings(require("dplyr"))) {
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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.rsi() %>%
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pull(amox_mic) %>%
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is.rsi()))
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}
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expect_equal(as.character(
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as.rsi(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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"S")
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expect_equal(as.character(
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as.rsi(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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"I")
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expect_equal(as.character(
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as.rsi(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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"R")
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if (suppressWarnings(require("dplyr"))) {
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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.rsi(guideline = "CLSI") %>%
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pull(amox_disk) %>%
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is.rsi())
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}
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# frequency tables
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if (suppressWarnings(require("cleaner"))) {
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expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
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}
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df <- data.frame(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") # note about cleaning
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expect_inherits(suppressWarnings(as.rsi(df)),
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"data.frame")
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expect_inherits(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
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amoxi = c("R", "S", "I", "invalid")))$amoxi),
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"rsi")
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expect_warning(as.rsi(data.frame(mo = "E. coli",
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NIT = c("<= 2", 32))))
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expect_message(as.rsi(data.frame(mo = "E. coli",
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NIT = c("<= 2", 32),
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uti = TRUE)))
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expect_message(as.rsi(data.frame(mo = "E. coli",
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NIT = c("<= 2", 32),
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specimen = c("urine", "blood"))))
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