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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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18
tests/testthat/test-rsi.R
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@@ -84,18 +84,20 @@ test_that("mic2rsi works", {
skip_on_cran()
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(as.character(
as.rsi(x = as.mic(0.125),
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "EUCAST")),
"S")
as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
mo = "B_STRPT_PNMN",
ab = "AMP",
guideline = "EUCAST 2020")),
c("S", "S", "I", "I", "R"))
# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
expect_equal(as.character(
as.rsi(x = as.mic(4),
as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "EUCAST")),
"I")
guideline = "CLSI 2019")),
c("S", "S", "I", "R", "R"))
# cutoffs at MIC = 8
expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),