AMR/tests/testthat/test-count.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# 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. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
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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$AMX))
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library(dplyr)
expect_equal(example_isolates %>% count_S(AMC), 1342)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE) +
example_isolates %>% count_IR(AMC, GEN, only_all_tested = TRUE))
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# count of cases
expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
summarise(cipro = count_SI(CIP),
genta = count_SI(GEN),
combination = count_SI(CIP, GEN)) %>%
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pull(combination),
c(253, 465, 192, 558))
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# count_df
expect_equal(
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
c(example_isolates$AMX %>% count_SI(),
example_isolates$AMX %>% count_R())
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)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_IR())
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)
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expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_I(),
example_isolates$AMX %>% count_R())
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)
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# 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)))
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# 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")))
expect_error(count_df(example_isolates[,"date"]))
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})