mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 13:26:11 +01:00
48 lines
2.4 KiB
R
Executable File
48 lines
2.4 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License version 2.0 for more details. #
|
|
# ==================================================================== #
|
|
|
|
context("mdro.R")
|
|
|
|
test_that("mdro works", {
|
|
library(dplyr)
|
|
|
|
expect_error(suppressWarnings(mdro(septic_patients, "invalid", col_mo = "mo", info = TRUE)))
|
|
expect_error(suppressWarnings(mdro(septic_patients, "fr", info = TRUE)))
|
|
expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
|
|
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
|
|
|
|
outcome <- suppressWarnings(mdro(septic_patients))
|
|
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
|
|
# check class
|
|
expect_equal(outcome %>% class(), c('ordered', 'factor'))
|
|
|
|
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),
|
|
c(1989, 9, 2)) # 1989 neg, 9 pos, 2 unconfirmed
|
|
|
|
expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
|
|
|
|
# still working on German guidelines
|
|
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
|
|
|
|
})
|