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(v0.7.1.9063) septic_patients -> example_isolates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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68
tests/testthat/test-count.R
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@ -22,27 +22,27 @@
context("count.R")
test_that("counts work", {
# AMX resistance in `septic_patients`
expect_equal(count_R(septic_patients$AMX), 683)
expect_equal(count_I(septic_patients$AMX), 3)
expect_equal(count_S(septic_patients$AMX), 543)
expect_equal(count_R(septic_patients$AMX) + count_I(septic_patients$AMX),
count_IR(septic_patients$AMX))
expect_equal(count_S(septic_patients$AMX) + count_I(septic_patients$AMX),
count_SI(septic_patients$AMX))
# AMX resistance in `example_isolates`
expect_equal(count_R(example_isolates$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))
library(dplyr)
expect_equal(septic_patients %>% count_S(AMC), 1342)
expect_equal(septic_patients %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
expect_equal(septic_patients %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
expect_equal(septic_patients %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
expect_equal(septic_patients %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
expect_identical(septic_patients %>% count_all(AMC, GEN, only_all_tested = TRUE),
septic_patients %>% count_S(AMC, GEN, only_all_tested = TRUE) +
septic_patients %>% count_IR(AMC, GEN, only_all_tested = TRUE))
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))
# count of cases
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro = count_SI(CIP),
genta = count_SI(GEN),
@ -52,29 +52,29 @@ test_that("counts work", {
# count_df
expect_equal(
septic_patients %>% select(AMX) %>% count_df() %>% pull(value),
c(septic_patients$AMX %>% count_SI(),
septic_patients$AMX %>% count_R())
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
c(example_isolates$AMX %>% count_SI(),
example_isolates$AMX %>% count_R())
)
expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_IR())
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_IR())
)
expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_I(),
septic_patients$AMX %>% count_R())
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_I(),
example_isolates$AMX %>% count_R())
)
# warning for speed loss
expect_warning(count_R(as.character(septic_patients$AMC)))
expect_warning(count_I(as.character(septic_patients$AMC)))
expect_warning(count_S(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_warning(count_S(septic_patients$AMC,
as.character(septic_patients$GEN)))
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)))
# check for errors
expect_error(count_IR("test", minimum = "test"))
@ -85,6 +85,6 @@ test_that("counts work", {
expect_error(count_S("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(septic_patients[,"date"]))
expect_error(count_df(example_isolates[,"date"]))
})