mirror of https://github.com/msberends/AMR.git
108 lines
4.5 KiB
R
Executable File
108 lines
4.5 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(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
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expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
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expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
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expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
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outcome <- mdro(example_isolates)
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outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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outcome <- mdro(example_isolates, "nl", info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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# example_isolates 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(brmo(example_isolates, info = FALSE),
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mdro(example_isolates, guideline = "BRMO", info = FALSE))
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# still working on German guidelines
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expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
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# test Dutch P. aeruginosa MDRO
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expect_equal(
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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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guideline = "BRMO",
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col_mo = "mo",
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info = FALSE)),
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"Negative")
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expect_equal(
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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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guideline = "BRMO",
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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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# 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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example_isolates %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
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count_R(example_isolates$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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#)
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,
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2)
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})
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