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(v1.6.0.9023) new unit test flow

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dr. M.S. (Matthijs) Berends
2021-05-13 19:31:47 +02:00
parent 655b813e99
commit aeea00881e
34 changed files with 408 additions and 355 deletions
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85
tests/testthat/test-proportion.R
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@ -52,30 +52,49 @@ test_that("proportions works", {
0.9382647,
tolerance = 0.0001)
library(dplyr)
# percentages
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(R = proportion_R(CIP, as_percent = TRUE),
I = proportion_I(CIP, as_percent = TRUE),
S = proportion_S(CIP, as_percent = TRUE),
n = n_rsi(CIP),
total = n()) %>%
pull(n) %>%
sum(),
1409)
# count of cases
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE),
cipro_n = n_rsi(CIP),
genta_p = proportion_SI(GEN, as_percent = TRUE),
genta_n = n_rsi(GEN),
combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
combination_n = n_rsi(CIP, GEN)) %>%
pull(combination_n),
c(305, 617, 241, 711))
if (require("dplyr")) {
# percentages
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(R = proportion_R(CIP, as_percent = TRUE),
I = proportion_I(CIP, as_percent = TRUE),
S = proportion_S(CIP, as_percent = TRUE),
n = n_rsi(CIP),
total = n()) %>%
pull(n) %>%
sum(),
1409)
# count of cases
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE),
cipro_n = n_rsi(CIP),
genta_p = proportion_SI(GEN, as_percent = TRUE),
genta_n = n_rsi(GEN),
combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
combination_n = n_rsi(CIP, GEN)) %>%
pull(combination_n),
c(305, 617, 241, 711))
# proportion_df
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
c(example_isolates$AMX %>% proportion_SI(),
example_isolates$AMX %>% proportion_R())
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% proportion_S(),
example_isolates$AMX %>% proportion_IR())
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% proportion_S(),
example_isolates$AMX %>% proportion_I(),
example_isolates$AMX %>% proportion_R())
)
}
reset_all_thrown_messages()
expect_warning(proportion_R(as.character(example_isolates$AMC)))
@ -115,24 +134,6 @@ test_that("proportions works", {
expect_warning(proportion_I(as.character(example_isolates$GEN)))
reset_all_thrown_messages()
expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
# proportion_df
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
c(example_isolates$AMX %>% proportion_SI(),
example_isolates$AMX %>% proportion_R())
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% proportion_S(),
example_isolates$AMX %>% proportion_IR())
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% proportion_S(),
example_isolates$AMX %>% proportion_I(),
example_isolates$AMX %>% proportion_R())
)
expect_error(proportion_df(c("A", "B", "C")))
expect_error(proportion_df(example_isolates[, "date"]))