mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 22:46:11 +01:00
91 lines
4.3 KiB
R
91 lines
4.3 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 `example_isolates`
|
|
expect_equal(count_R(example_isolates$AMX), 683)
|
|
expect_equal(count_I(example_isolates$AMX), 3)
|
|
expect_equal(count_S(example_isolates$AMX), 543)
|
|
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
|
|
count_IR(example_isolates$AMX))
|
|
expect_equal(count_S(example_isolates$AMX) + count_I(example_isolates$AMX),
|
|
count_SI(example_isolates$AMX))
|
|
|
|
library(dplyr)
|
|
expect_equal(example_isolates %>% count_S(AMC), 1342)
|
|
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
|
|
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
|
|
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
|
|
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
|
|
expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
|
|
example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE) +
|
|
example_isolates %>% count_IR(AMC, GEN, only_all_tested = TRUE))
|
|
|
|
# count of cases
|
|
expect_equal(example_isolates %>%
|
|
group_by(hospital_id) %>%
|
|
summarise(cipro = count_SI(CIP),
|
|
genta = count_SI(GEN),
|
|
combination = count_SI(CIP, GEN)) %>%
|
|
pull(combination),
|
|
c(253, 465, 192, 558))
|
|
|
|
# count_df
|
|
expect_equal(
|
|
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
|
|
c(example_isolates$AMX %>% count_SI(),
|
|
example_isolates$AMX %>% count_R())
|
|
)
|
|
expect_equal(
|
|
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
|
|
c(example_isolates$AMX %>% count_S(),
|
|
example_isolates$AMX %>% count_IR())
|
|
)
|
|
expect_equal(
|
|
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
|
|
c(example_isolates$AMX %>% count_S(),
|
|
example_isolates$AMX %>% count_I(),
|
|
example_isolates$AMX %>% count_R())
|
|
)
|
|
|
|
# warning for speed loss
|
|
expect_warning(count_R(as.character(example_isolates$AMC)))
|
|
expect_warning(count_I(as.character(example_isolates$AMC)))
|
|
expect_warning(count_S(as.character(example_isolates$AMC,
|
|
example_isolates$GEN)))
|
|
expect_warning(count_S(example_isolates$AMC,
|
|
as.character(example_isolates$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(example_isolates[,"date"]))
|
|
|
|
})
|