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(v0.7.1.9063) septic_patients -> example_isolates
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@ -30,15 +30,15 @@ test_that("EUCAST rules work", {
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"then_change_these_antibiotics", "to_value",
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"reference.rule", "reference.rule_group"))
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expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
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expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
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expect_error(eucast_rules(x = "text"))
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expect_error(eucast_rules(data.frame(a = "test")))
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expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
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expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S")))
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expect_identical(colnames(septic_patients),
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colnames(suppressWarnings(eucast_rules(septic_patients))))
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expect_identical(colnames(example_isolates),
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colnames(suppressWarnings(eucast_rules(example_isolates))))
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a <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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@ -66,7 +66,7 @@ test_that("EUCAST rules work", {
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# piperacillin must be R in Enterobacteriaceae when tica is R
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library(dplyr)
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expect_equal(suppressWarnings(
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septic_patients %>%
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example_isolates %>%
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mutate(TIC = as.rsi("R"),
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PIP = as.rsi("S")) %>%
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eucast_rules(col_mo = "mo") %>%
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@ -79,7 +79,7 @@ test_that("EUCAST rules work", {
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# Azithromicin and Clarythromycin must be equal to Erythromycin
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a <- suppressWarnings(
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septic_patients %>%
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example_isolates %>%
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transmute(mo,
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ERY,
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AZM = as.rsi("R"),
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@ -87,7 +87,7 @@ test_that("EUCAST rules work", {
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eucast_rules(col_mo = "mo") %>%
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pull(CLR))
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b <- suppressWarnings(
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septic_patients %>%
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example_isolates %>%
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select(mo, ERY) %>%
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eucast_rules(col_mo = "mo") %>%
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pull(ERY))
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@ -108,9 +108,9 @@ test_that("EUCAST rules work", {
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"S")
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# also test norf
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expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(NOR = "S", NAL = "S"))))
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expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"))))
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# check verbose output
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expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
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expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE)))
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})
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