2018-04-18 12:24:54 +02:00
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context("eucast.R")
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2018-03-27 17:43:42 +02:00
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test_that("EUCAST rules work", {
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2018-08-29 16:25:57 +02:00
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expect_error(EUCAST_rules(septic_patients, col_bactid = "Non-existing"))
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2018-07-23 14:14:03 +02:00
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expect_identical(colnames(septic_patients),
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colnames(suppressWarnings(EUCAST_rules(septic_patients))))
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2018-05-02 14:56:25 +02:00
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2018-07-23 14:14:03 +02:00
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a <- data.frame(bactid =
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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2018-03-27 17:43:42 +02:00
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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2018-07-23 14:14:03 +02:00
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b <- data.frame(bactid =
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2018-07-26 16:30:42 +02:00
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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2018-03-27 17:43:42 +02:00
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amox = "R", # Amoxicillin
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stringsAsFactors = FALSE)
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2018-07-30 00:57:49 +02:00
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expect_warning(EUCAST_rules(a, info = FALSE))
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expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
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2018-07-23 14:14:03 +02:00
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expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
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2018-04-02 16:05:09 +02:00
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2018-07-23 14:14:03 +02:00
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a <- data.frame(bactid =
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c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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2018-03-27 17:43:42 +02:00
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coli = "-", # Colistin
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stringsAsFactors = FALSE)
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2018-07-23 14:14:03 +02:00
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b <- data.frame(bactid =
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2018-07-26 16:30:42 +02:00
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c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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2018-03-27 17:43:42 +02:00
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coli = "R", # Colistin
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stringsAsFactors = FALSE)
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2018-07-30 00:57:49 +02:00
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expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
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2018-08-29 16:25:57 +02:00
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# pita 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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mutate(tica = as.rsi("R"),
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pita = as.rsi("S")) %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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left_join_microorganisms() %>%
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filter(family == "Enterobacteriaceae") %>%
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pull(pita) %>%
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unique() %>%
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as.character()),
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"R")
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# azit and clar must be equal to eryt
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expect_equal(suppressWarnings(
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septic_patients %>%
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mutate(azit = as.rsi("R"),
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clar = as.rsi("R")) %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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pull(clar)),
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suppressWarnings(
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septic_patients %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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left_join_microorganisms() %>%
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pull(eryt)))
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2018-03-27 17:43:42 +02:00
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})
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