AMR/tests/testthat/test-count.R

84 lines
3.8 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.gitab.io/AMR. #
# ==================================================================== #
context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
expect_equal(count_R(septic_patients$amox), 683)
expect_equal(count_I(septic_patients$amox), 3)
expect_equal(count_S(septic_patients$amox), 543)
expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
count_IR(septic_patients$amox))
expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
count_SI(septic_patients$amox))
library(dplyr)
expect_equal(septic_patients %>% count_S(amcl), 1342)
expect_equal(septic_patients %>% count_S(amcl, gent), 1660)
expect_equal(septic_patients %>% count_all(amcl, gent), 1798)
expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro = count_S(cipr),
genta = count_S(gent),
combination = count_S(cipr, gent)) %>%
pull(combination),
c(192, 446, 184, 474))
# count_df
expect_equal(
septic_patients %>% select(amox) %>% count_df() %>% pull(Value),
c(septic_patients$amox %>% count_S(),
septic_patients$amox %>% count_I(),
septic_patients$amox %>% count_R())
)
expect_equal(
septic_patients %>% select(amox) %>% count_df(combine_IR = TRUE) %>% pull(Value),
c(septic_patients$amox %>% count_S(),
septic_patients$amox %>% count_IR())
)
# warning for speed loss
expect_warning(count_R(as.character(septic_patients$amcl)))
expect_warning(count_I(as.character(septic_patients$amcl)))
expect_warning(count_S(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_warning(count_S(septic_patients$amcl,
as.character(septic_patients$gent)))
# 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"]))
})