mirror of https://github.com/msberends/AMR.git
79 lines
2.7 KiB
R
Executable File
79 lines
2.7 KiB
R
Executable File
context("eucast.R")
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test_that("EUCAST rules work", {
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expect_error(EUCAST_rules(septic_patients, col_mo = "Non-existing"))
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expect_identical(colnames(septic_patients),
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colnames(suppressWarnings(EUCAST_rules(septic_patients))))
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a <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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amox = "R", # Amoxicillin
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stringsAsFactors = FALSE)
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expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
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expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
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a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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coli = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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coli = "R", # Colistin
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stringsAsFactors = FALSE)
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expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
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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_mo = "mo") %>%
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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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a <- suppressWarnings(
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septic_patients %>%
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transmute(mo,
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eryt,
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azit = as.rsi("R"),
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clar = as.rsi("R")) %>%
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EUCAST_rules(col_mo = "mo") %>%
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pull(clar))
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b <- suppressWarnings(
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septic_patients %>%
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select(mo, eryt) %>%
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EUCAST_rules(col_mo = "mo") %>%
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pull(eryt))
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expect_identical(a[!is.na(b)],
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b[!is.na(b)])
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# amox is inferred by benzylpenicillin in Kingella kingae
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expect_equal(
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as.list(EUCAST_rules(
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data.frame(mo = as.mo("Kingella kingae"),
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peni = "S",
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amox = "-",
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stringsAsFactors = FALSE)
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, info = FALSE))$amox,
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"S")
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expect_output(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
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})
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