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159 lines
6.7 KiB
159 lines
6.7 KiB
# ==================================================================== # |
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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 (AMR:::pkg_is_available("ggplot2")) { |
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expect_inherits(autoplot(as.rsi(c("S", "I", "R"))), "gg") |
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} |
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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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as.logical(lapply(example_isolates, is.rsi))) |
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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 (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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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 (AMR:::pkg_is_available("skimr")) { |
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expect_inherits(skim(example_isolates), |
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"data.frame") |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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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 (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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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 (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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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 (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(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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