P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-12-15 12:30:22 +01:00
Code Releases Activity

(v0.7.1.9063) septic_patients -> example_isolates

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

78
tests/testthat/test-portion.R
View File

@@ -22,28 +22,28 @@
context("portion.R")
test_that("portions works", {
# AMX resistance in `septic_patients`
expect_equal(portion_R(septic_patients$AMX), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$AMX), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$AMX) - portion_I(septic_patients$AMX),
portion_S(septic_patients$AMX))
expect_equal(portion_R(septic_patients$AMX) + portion_I(septic_patients$AMX),
portion_IR(septic_patients$AMX))
expect_equal(portion_S(septic_patients$AMX) + portion_I(septic_patients$AMX),
portion_SI(septic_patients$AMX))
# AMX resistance in `example_isolates`
expect_equal(portion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(example_isolates$AMX) - portion_I(example_isolates$AMX),
portion_S(example_isolates$AMX))
expect_equal(portion_R(example_isolates$AMX) + portion_I(example_isolates$AMX),
portion_IR(example_isolates$AMX))
expect_equal(portion_S(example_isolates$AMX) + portion_I(example_isolates$AMX),
portion_SI(example_isolates$AMX))
expect_equal(septic_patients %>% portion_SI(AMC),
expect_equal(example_isolates %>% portion_SI(AMC),
0.7626397,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_SI(AMC, GEN),
expect_equal(example_isolates %>% portion_SI(AMC, GEN),
0.9408,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_SI(AMC, GEN, only_all_tested = TRUE),
expect_equal(example_isolates %>% portion_SI(AMC, GEN, only_all_tested = TRUE),
0.9382647,
tolerance = 0.0001)
# percentages
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(R = portion_R(CIP, as_percent = TRUE),
I = portion_I(CIP, as_percent = TRUE),
@@ -55,7 +55,7 @@ test_that("portions works", {
1409)
# count of cases
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro_p = portion_SI(CIP, as_percent = TRUE),
cipro_n = n_rsi(CIP),
@@ -66,14 +66,14 @@ test_that("portions works", {
pull(combination_n),
c(305, 617, 241, 711))
expect_warning(portion_R(as.character(septic_patients$AMC)))
expect_warning(portion_S(as.character(septic_patients$AMC)))
expect_warning(portion_S(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_warning(n_rsi(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$AMC,
septic_patients$GEN))),
expect_warning(portion_R(as.character(example_isolates$AMC)))
expect_warning(portion_S(as.character(example_isolates$AMC)))
expect_warning(portion_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_warning(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN))),
1879)
# check for errors
@@ -86,36 +86,36 @@ test_that("portions works", {
expect_error(portion_S("test", also_single_tested = TRUE))
# check too low amount of isolates
expect_identical(suppressWarnings(portion_R(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
expect_identical(suppressWarnings(portion_I(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
expect_identical(suppressWarnings(portion_S(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
# warning for speed loss
expect_warning(portion_R(as.character(septic_patients$GEN)))
expect_warning(portion_I(as.character(septic_patients$GEN)))
expect_warning(portion_S(septic_patients$AMC, as.character(septic_patients$GEN)))
expect_warning(portion_R(as.character(example_isolates$GEN)))
expect_warning(portion_I(as.character(example_isolates$GEN)))
expect_warning(portion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
# portion_df
expect_equal(
septic_patients %>% select(AMX) %>% portion_df() %>% pull(value),
c(septic_patients$AMX %>% portion_SI(),
septic_patients$AMX %>% portion_R())
example_isolates %>% select(AMX) %>% portion_df() %>% pull(value),
c(example_isolates$AMX %>% portion_SI(),
example_isolates$AMX %>% portion_R())
)
expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_IR())
example_isolates %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% portion_S(),
example_isolates$AMX %>% portion_IR())
)
expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_I(),
septic_patients$AMX %>% portion_R())
example_isolates %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% portion_S(),
example_isolates$AMX %>% portion_I(),
example_isolates$AMX %>% portion_R())
)
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
expect_error(portion_df(example_isolates[,"date"]))
})