mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 06:46:12 +01:00
110 lines
4.9 KiB
R
110 lines
4.9 KiB
R
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
|
|
# Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# 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. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
|
|
expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
|
|
expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))
|
|
|
|
# AMX resistance in `example_isolates`
|
|
expect_equal(count_R(example_isolates$AMX), 804)
|
|
expect_equal(count_I(example_isolates$AMX), 3)
|
|
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
|
|
expect_equal(
|
|
count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
|
|
suppressWarnings(count_IR(example_isolates$AMX))
|
|
)
|
|
expect_equal(
|
|
suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
|
|
count_SI(example_isolates$AMX)
|
|
)
|
|
|
|
# warning for speed loss
|
|
# expect_warning(count_resistant(as.character(example_isolates$AMC)))
|
|
|
|
# expect_warning(count_resistant(example_isolates$AMC, as.character(example_isolates$GEN)))
|
|
|
|
# check for errors
|
|
expect_error(count_resistant("test", minimum = "test"))
|
|
expect_error(count_resistant("test", as_percent = "test"))
|
|
expect_error(count_susceptible("test", minimum = "test"))
|
|
expect_error(count_susceptible("test", as_percent = "test"))
|
|
|
|
expect_error(count_df(c("A", "B", "C")))
|
|
expect_error(count_df(example_isolates[, "date", drop = TRUE]))
|
|
|
|
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
|
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
|
|
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
|
|
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
|
|
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_susceptible(AMC, GEN, only_all_tested = TRUE) +
|
|
example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)
|
|
)
|
|
|
|
# count of cases
|
|
expect_equal(
|
|
example_isolates %>%
|
|
group_by(ward) %>%
|
|
summarise(
|
|
cipro = count_susceptible(CIP),
|
|
genta = count_susceptible(GEN),
|
|
combination = count_susceptible(CIP, GEN)
|
|
) %>%
|
|
pull(combination),
|
|
c(946, 428, 94)
|
|
)
|
|
|
|
# count_df
|
|
expect_equal(
|
|
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
|
|
c(
|
|
example_isolates$AMX %>% count_susceptible(),
|
|
example_isolates$AMX %>% count_resistant()
|
|
)
|
|
)
|
|
expect_equal(
|
|
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
|
|
c(
|
|
suppressWarnings(example_isolates$AMX %>% count_S()),
|
|
example_isolates$AMX %>% count_I(),
|
|
example_isolates$AMX %>% count_R()
|
|
)
|
|
)
|
|
|
|
# grouping in sir_calc_df() (= backbone of sir_df())
|
|
expect_true("ward" %in% (example_isolates %>%
|
|
group_by(ward) %>%
|
|
select(ward, AMX, CIP, gender) %>%
|
|
sir_df() %>%
|
|
colnames()))
|
|
}
|