mirror of https://github.com/msberends/AMR.git
113 lines
4.6 KiB
R
Executable File
113 lines
4.6 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("mdro.R")
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test_that("mdro works", {
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library(dplyr)
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expect_error(suppressWarnings(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE)))
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expect_error(suppressWarnings(mdro(septic_patients, country = "fr", info = TRUE)))
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expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
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expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
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outcome <- suppressWarnings(mdro(septic_patients))
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outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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# septic_patients should have these finding using Dutch guidelines
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expect_equal(outcome %>% freq() %>% pull(count),
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c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
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expect_equal(
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suppressWarnings(
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brmo(septic_patients, info = FALSE)),
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suppressWarnings(
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mdro(septic_patients, country = "nl", info = FALSE)
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)
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)
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# still working on German guidelines
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expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
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# test Dutch P. aeruginosa MDRO
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expect_equal(suppressWarnings(
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
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cfta = "S",
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cipr = "S",
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mero = "S",
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imip = "S",
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gent = "S",
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tobr = "S",
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pita = "S"),
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country = "nl",
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col_mo = "mo",
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info = FALSE))
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), "Negative")
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expect_equal(suppressWarnings(
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
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cefta = "R",
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cipr = "R",
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mero = "R",
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imip = "R",
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gent = "R",
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tobr = "R",
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pita = "R"),
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country = "nl",
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col_mo = "mo",
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info = FALSE))
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), "Positive")
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# MDR TB
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expect_equal(
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suppressWarnings(
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# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
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# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
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septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2]
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),
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count_R(septic_patients$RIF))
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sample_rsi <- function() {
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sample(c("S", "I", "R"),
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size = 5000,
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prob = c(0.5, 0.1, 0.4),
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replace = TRUE)
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}
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expect_gt(
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suppressWarnings(
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data.frame(rifampicin = sample_rsi(),
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inh = sample_rsi(),
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gatifloxacin = sample_rsi(),
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eth = sample_rsi(),
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pza = sample_rsi(),
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MFX = sample_rsi(),
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KAN = sample_rsi()) %>%
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mdr_tb() %>%
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n_distinct()),
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2)
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})
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