mirror of https://github.com/msberends/AMR.git
89 lines
4.0 KiB
R
89 lines
4.0 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
context("count.R")
|
|
|
|
test_that("counts work", {
|
|
# AMX resistance in `septic_patients`
|
|
expect_equal(count_R(septic_patients$AMX), 683)
|
|
expect_equal(count_I(septic_patients$AMX), 3)
|
|
expect_equal(count_S(septic_patients$AMX), 543)
|
|
expect_equal(count_R(septic_patients$AMX) + count_I(septic_patients$AMX),
|
|
count_IR(septic_patients$AMX))
|
|
expect_equal(count_S(septic_patients$AMX) + count_I(septic_patients$AMX),
|
|
count_SI(septic_patients$AMX))
|
|
|
|
library(dplyr)
|
|
expect_equal(septic_patients %>% count_S(AMC), 1342)
|
|
expect_equal(septic_patients %>% count_S(AMC, GEN), 1660)
|
|
expect_equal(septic_patients %>% count_all(AMC, GEN), 1798)
|
|
expect_identical(septic_patients %>% count_all(AMC, GEN),
|
|
septic_patients %>% count_S(AMC, GEN) +
|
|
septic_patients %>% count_IR(AMC, GEN))
|
|
|
|
# count of cases
|
|
expect_equal(septic_patients %>%
|
|
group_by(hospital_id) %>%
|
|
summarise(cipro = count_S(CIP),
|
|
genta = count_S(GEN),
|
|
combination = count_S(CIP, GEN)) %>%
|
|
pull(combination),
|
|
c(192, 446, 184, 474))
|
|
|
|
# count_df
|
|
expect_equal(
|
|
septic_patients %>% select(AMX) %>% count_df() %>% pull(value),
|
|
c(septic_patients$AMX %>% count_SI(),
|
|
septic_patients$AMX %>% count_R())
|
|
)
|
|
expect_equal(
|
|
septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
|
|
c(septic_patients$AMX %>% count_S(),
|
|
septic_patients$AMX %>% count_IR())
|
|
)
|
|
expect_equal(
|
|
septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
|
|
c(septic_patients$AMX %>% count_S(),
|
|
septic_patients$AMX %>% count_I(),
|
|
septic_patients$AMX %>% count_R())
|
|
)
|
|
|
|
# warning for speed loss
|
|
expect_warning(count_R(as.character(septic_patients$AMC)))
|
|
expect_warning(count_I(as.character(septic_patients$AMC)))
|
|
expect_warning(count_S(as.character(septic_patients$AMC,
|
|
septic_patients$GEN)))
|
|
expect_warning(count_S(septic_patients$AMC,
|
|
as.character(septic_patients$GEN)))
|
|
|
|
# check for errors
|
|
expect_error(count_IR("test", minimum = "test"))
|
|
expect_error(count_IR("test", as_percent = "test"))
|
|
expect_error(count_I("test", minimum = "test"))
|
|
expect_error(count_I("test", as_percent = "test"))
|
|
expect_error(count_S("test", minimum = "test"))
|
|
expect_error(count_S("test", as_percent = "test"))
|
|
|
|
expect_error(count_df(c("A", "B", "C")))
|
|
expect_error(count_df(septic_patients[,"date"]))
|
|
|
|
})
|