mirror of https://github.com/msberends/AMR.git
117 lines
4.8 KiB
R
Executable File
117 lines
4.8 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("eucast_rules.R")
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test_that("EUCAST rules work", {
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# thoroughly check input table
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expect_equal(colnames(eucast_rules_file),
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c("if_mo_property", "like.is.one_of", "this_value",
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"and_these_antibiotics", "have_these_values",
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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(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(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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"Enterobacter aerogenes"),
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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"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, "mo", info = FALSE)), b)
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expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
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a <- data.frame(mo = c("Staphylococcus aureus",
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"Streptococcus group A"),
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COL = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("Staphylococcus aureus",
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"Streptococcus group A"),
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COL = "R", # Colistin
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stringsAsFactors = FALSE)
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expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
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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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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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left_join_microorganisms() %>%
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filter(family == "Enterobacteriaceae") %>%
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pull(PIP) %>%
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unique() %>%
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as.character()),
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"R")
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# Azithromicin and Clarythromycin must be equal to Erythromycin
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a <- suppressWarnings(
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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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CLR = as.rsi("R")) %>%
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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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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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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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suppressWarnings(
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as.list(eucast_rules(
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data.frame(mo = as.mo("Kingella kingae"),
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PEN = "S",
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AMX = "-",
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stringsAsFactors = FALSE)
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, info = FALSE))$AMX
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),
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"S")
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# also test norf
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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(example_isolates, verbose = TRUE)))
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})
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