AMR/tests/testthat/test-mdro.R

108 lines
4.4 KiB
R
Raw Normal View History

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
2019-01-02 23:24:07 +01:00
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
2019-01-02 23:24:07 +01:00
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
2019-01-02 23:24:07 +01:00
# 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. #
2019-04-05 18:47:39 +02:00
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mdro.R")
2018-11-16 20:50:50 +01:00
test_that("mdro works", {
library(dplyr)
2019-06-03 17:45:22 +02:00
expect_error(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE))
expect_error(mdro(septic_patients, country = "fr", info = TRUE))
expect_error(mdro(septic_patients, country = c("de", "nl"), info = TRUE))
expect_error(mdro(septic_patients, col_mo = "invalid", info = TRUE))
2019-06-03 17:45:22 +02:00
outcome <- mdro(septic_patients)
outcome <- eucast_exceptional_phenotypes(septic_patients, info = TRUE)
2018-04-25 15:33:58 +02:00
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
2019-06-03 17:45:22 +02:00
outcome <- 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),
2019-05-20 19:12:41 +02:00
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
2019-06-03 17:45:22 +02:00
expect_equal(brmo(septic_patients, info = FALSE),
mdro(septic_patients, country = "nl", info = FALSE))
# still working on German guidelines
2018-11-16 20:50:50 +01:00
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
2019-04-09 14:59:17 +02:00
# test Dutch P. aeruginosa MDRO
2019-06-03 17:45:22 +02:00
expect_equal(
2019-04-09 14:59:17 +02:00
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cfta = "S",
cipr = "S",
mero = "S",
imip = "S",
gent = "S",
tobr = "S",
pita = "S"),
country = "nl",
col_mo = "mo",
2019-06-03 17:45:22 +02:00
info = FALSE)),
"Negative")
expect_equal(
2019-04-09 14:59:17 +02:00
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cefta = "R",
cipr = "R",
mero = "R",
imip = "R",
gent = "R",
tobr = "R",
pita = "R"),
country = "nl",
col_mo = "mo",
2019-06-03 17:45:22 +02:00
info = FALSE)),
"Positive")
2019-04-09 14:59:17 +02:00
2019-05-23 16:58:59 +02:00
# MDR TB
expect_equal(
2019-06-03 17:45:22 +02:00
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
2019-05-23 16:58:59 +02:00
count_R(septic_patients$RIF))
sample_rsi <- function() {
sample(c("S", "I", "R"),
size = 5000,
prob = c(0.5, 0.1, 0.4),
replace = TRUE)
}
expect_gt(
2019-06-03 17:45:22 +02:00
#suppressWarnings(
2019-05-23 16:58:59 +02:00
data.frame(rifampicin = sample_rsi(),
inh = sample_rsi(),
gatifloxacin = sample_rsi(),
eth = sample_rsi(),
pza = sample_rsi(),
MFX = sample_rsi(),
KAN = sample_rsi()) %>%
mdr_tb() %>%
2019-06-03 17:45:22 +02:00
n_distinct()
#)
,
2019-05-23 16:58:59 +02:00
2)
})