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global var fix

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dr. M.S. (Matthijs) Berends
2019-02-27 17:39:39 +01:00
parent 642f6571fe
commit 95c49fdf79
10 changed files with 314 additions and 299 deletions
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20
tests/testthat/test-eucast_rules.R
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@ -28,26 +28,26 @@ test_that("EUCAST rules work", {
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(eucast_rules(septic_patients))))
a <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
coli = "-", # Colistin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
b <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)