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first inclusion of ITIS data

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-24 23:33:29 +02:00
parent df5d82fff3
commit 9c566585b0
29 changed files with 734 additions and 466 deletions
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10
tests/testthat/test-count.R
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@ -2,16 +2,16 @@ context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
expect_equal(count_R(septic_patients$amox), 659)
expect_equal(count_R(septic_patients$amox), 662)
expect_equal(count_I(septic_patients$amox), 3)
expect_equal(count_S(septic_patients$amox), 336)
expect_equal(count_S(septic_patients$amox), 335)
expect_equal(count_R(septic_patients$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))
expect_equal(septic_patients %>% count_S(amcl), 1056)
expect_equal(septic_patients %>% count_S(amcl, gent), 1385)
expect_equal(septic_patients %>% count_S(amcl), 1057)
expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
# count of cases
expect_equal(septic_patients %>%
@ -20,7 +20,7 @@ test_that("counts work", {
genta = count_S(gent),
combination = count_S(cipr, gent)) %>%
pull(combination),
c(192, 440, 184, 474))
c(192, 446, 184, 474))
expect_equal(septic_patients %>% select(amox, cipr) %>% count_df(translate_ab = "official") %>% nrow(),
6)