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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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80
inst/tinytest/test-count.R
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@ -9,7 +9,7 @@
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@ -31,16 +31,22 @@ expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
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$AMX))
expect_equal(
count_R(example_isolates$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)))
expect_warning(count_resistant(
example_isolates$AMC,
as.character(example_isolates$GEN)
))
# check for errors
expect_error(count_resistant("test", minimum = "test"))
@ -57,41 +63,53 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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))
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(253, 465, 192, 558))
expect_equal(
example_isolates %>%
group_by(ward) %>%
summarise(
cipro = count_susceptible(CIP),
genta = count_susceptible(GEN),
combination = count_susceptible(CIP, GEN)
) %>%
pull(combination),
c(253, 465, 192, 558)
)
# count_df
expect_equal(
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
c(example_isolates$AMX %>% count_susceptible(),
example_isolates$AMX %>% count_resistant())
c(
example_isolates$AMX %>% count_susceptible(),
example_isolates$AMX %>% count_resistant()
)
)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(suppressWarnings(example_isolates$AMX %>% count_S()),
suppressWarnings(example_isolates$AMX %>% count_IR()))
c(
suppressWarnings(example_isolates$AMX %>% count_S()),
suppressWarnings(example_isolates$AMX %>% count_IR())
)
)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(suppressWarnings(example_isolates$AMX %>% count_S()),
c(
suppressWarnings(example_isolates$AMX %>% count_S()),
example_isolates$AMX %>% count_I(),
example_isolates$AMX %>% count_R())
example_isolates$AMX %>% count_R()
)
)
# grouping in rsi_calc_df() (= backbone of rsi_df())
expect_true("ward" %in% (example_isolates %>%
group_by(ward) %>%
select(ward, AMX, CIP, gender) %>%
rsi_df() %>%
colnames()))
expect_true("ward" %in% (example_isolates %>%
group_by(ward) %>%
select(ward, AMX, CIP, gender) %>%
rsi_df() %>%
colnames()))
}