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new antibiotics

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dr. M.S. (Matthijs) Berends
2019-05-10 16:44:59 +02:00
parent 73f1ee1159
commit 68cc7ef0d0
147 changed files with 6228 additions and 4187 deletions
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60
tests/testthat/test-count.R
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@ -22,52 +22,52 @@
context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
expect_equal(count_R(septic_patients$amox), 683)
expect_equal(count_I(septic_patients$amox), 3)
expect_equal(count_S(septic_patients$amox), 543)
expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
count_IR(septic_patients$amox))
expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
count_SI(septic_patients$amox))
# AMX resistance in `septic_patients`
expect_equal(count_R(septic_patients$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))
library(dplyr)
expect_equal(septic_patients %>% count_S(amcl), 1342)
expect_equal(septic_patients %>% count_S(amcl, gent), 1660)
expect_equal(septic_patients %>% count_all(amcl, gent), 1798)
expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))
expect_equal(septic_patients %>% count_S(AMC), 1342)
expect_equal(septic_patients %>% count_S(AMC, GEN), 1660)
expect_equal(septic_patients %>% count_all(AMC, GEN), 1798)
expect_identical(septic_patients %>% count_all(AMC, GEN),
septic_patients %>% count_S(AMC, GEN) +
septic_patients %>% count_IR(AMC, GEN))
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro = count_S(cipr),
genta = count_S(gent),
combination = count_S(cipr, gent)) %>%
summarise(cipro = count_S(CIP),
genta = count_S(GEN),
combination = count_S(CIP, GEN)) %>%
pull(combination),
c(192, 446, 184, 474))
# count_df
expect_equal(
septic_patients %>% select(amox) %>% count_df() %>% pull(Value),
c(septic_patients$amox %>% count_S(),
septic_patients$amox %>% count_I(),
septic_patients$amox %>% count_R())
septic_patients %>% select(AMX) %>% count_df() %>% pull(Value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_I(),
septic_patients$AMX %>% count_R())
)
expect_equal(
septic_patients %>% select(amox) %>% count_df(combine_IR = TRUE) %>% pull(Value),
c(septic_patients$amox %>% count_S(),
septic_patients$amox %>% count_IR())
septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(Value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_IR())
)
# warning for speed loss
expect_warning(count_R(as.character(septic_patients$amcl)))
expect_warning(count_I(as.character(septic_patients$amcl)))
expect_warning(count_S(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_warning(count_S(septic_patients$amcl,
as.character(septic_patients$gent)))
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)))
# check for errors
expect_error(count_IR("test", minimum = "test"))