AMR/tests/testthat/test-count.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# ==================================================================== #
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context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
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expect_equal(count_R(septic_patients$amox), 683)
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expect_equal(count_I(septic_patients$amox), 3)
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expect_equal(count_S(septic_patients$amox), 486)
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expect_equal(count_R(septic_patients$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$amox))
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library(dplyr)
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expect_equal(septic_patients %>% count_S(amcl), 1291)
expect_equal(septic_patients %>% count_S(amcl, gent), 1609)
expect_equal(septic_patients %>% count_all(amcl, gent), 1747)
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expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))
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# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro = count_S(cipr),
genta = count_S(gent),
combination = count_S(cipr, gent)) %>%
pull(combination),
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c(192, 446, 184, 474))
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# count_df
expect_equal(
septic_patients %>% select(amox) %>% count_df() %>% pull(Value),
c(septic_patients$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())
)
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# 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"))
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expect_error(count_df(c("A", "B", "C")))
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expect_error(count_df(septic_patients[,"date"]))
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})