mirror of https://github.com/msberends/AMR.git
48 lines
2.4 KiB
R
Executable File
48 lines
2.4 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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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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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, "invalid", col_bactid = "mo", info = TRUE)))
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expect_error(suppressWarnings(mdro(septic_patients, "fr", col_bactid = "mo", 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(1989, 9, 2)) # 1989 neg, 9 pos, 2 unconfirmed
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expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
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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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})
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