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new EUCAST rules: clinical breakpoints

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dr. M.S. (Matthijs) Berends
2018-10-17 17:32:34 +02:00
parent d5a41de711
commit 693f64bdbf
20 changed files with 1165 additions and 171 deletions
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10
tests/testthat/test-count.R
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@ -2,18 +2,18 @@ context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
expect_equal(count_R(septic_patients$amox), 662)
expect_equal(count_R(septic_patients$amox), 683)
expect_equal(count_I(septic_patients$amox), 3)
expect_equal(count_S(septic_patients$amox), 335)
expect_equal(count_S(septic_patients$amox), 486)
expect_equal(count_R(septic_patients$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))
library(dplyr)
expect_equal(septic_patients %>% count_S(amcl), 1057)
expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
expect_equal(septic_patients %>% count_all(amcl, gent), 1517)
expect_equal(septic_patients %>% count_S(amcl), 1291)
expect_equal(septic_patients %>% count_S(amcl, gent), 1609)
expect_equal(septic_patients %>% count_all(amcl, gent), 1747)
expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))