AMR/tests/testthat/test-mdro.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# 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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# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
context("mdro.R")
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test_that("mdro works", {
library(dplyr)
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expect_error(suppressWarnings(mdro(septic_patients, "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, "fr", info = TRUE)))
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expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
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outcome <- suppressWarnings(mdro(septic_patients))
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
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# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
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outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
# septic_patients should have these finding using Dutch guidelines
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(
suppressWarnings(
brmo(septic_patients, info = FALSE)),
suppressWarnings(
mdro(septic_patients, "nl", info = FALSE)
)
)
# still working on German guidelines
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expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
})