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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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20
tests/testthat/test-portion.R
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@@ -2,8 +2,8 @@ context("portion.R")
test_that("portions works", {
# amox resistance in `septic_patients`
expect_equal(portion_R(septic_patients$amox), 0.662, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.003, tolerance = 0.0001)
expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.0025597, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
portion_S(septic_patients$amox))
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
@@ -12,17 +12,17 @@ test_that("portions works", {
portion_SI(septic_patients$amox))
expect_equal(septic_patients %>% portion_S(amcl),
0.6706853,
0.7062363,
tolerance = 0.001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.9202373,
0.9210074,
tolerance = 0.001)
# amcl+genta susceptibility around 92.1%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
septic_patients$gent,
interpretation = "S")),
0.9202373,
0.9210074,
tolerance = 0.000001)
# percentages
@@ -57,7 +57,7 @@ test_that("portions works", {
septic_patients$gent)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent))),
1576)
1828)
# check for errors
expect_error(portion_IR("test", minimum = "test"))
@@ -83,16 +83,16 @@ test_that("portions works", {
})
test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 66.33%
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.665, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.665, tolerance = 0.0001)
# amox resistance in `septic_patients` should be around 58.53%
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9540412,
0.9498886,
tolerance = 0.0001)
# count of cases