mirror of https://github.com/msberends/AMR.git
148 lines
7.0 KiB
R
Executable File
148 lines
7.0 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.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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skip_on_cran()
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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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"reference.version",
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"note"))
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MOs_mentioned <- unique(eucast_rules_file$this_value)
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MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_possibly_regex(MOs_mentioned)], ",", fixed = TRUE))))
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MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
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expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)
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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", stringsAsFactors = TRUE)))
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expect_identical(colnames(example_isolates),
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colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
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expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
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a <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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"Enterobacter cloacae"),
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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 cloacae"),
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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_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
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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, warn.conflicts = FALSE)
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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", version_expertrules = 3.1, info = FALSE) %>%
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left_join_microorganisms(by = "mo") %>%
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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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# Azithromycin and Clarythromycin must be equal to Erythromycin
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a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
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ERY = example_isolates$ERY,
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AZM = as.rsi("R"),
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CLR = factor("R"),
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stringsAsFactors = FALSE),
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version_expertrules = 3.1,
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only_rsi_columns = FALSE)$CLR))
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b <- example_isolates$ERY
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expect_identical(a[!is.na(b)],
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b[!is.na(b)])
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# amox is inferred by benzylpenicillin in Kingella kingae
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expect_equal(
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suppressWarnings(
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as.list(eucast_rules(
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data.frame(mo = as.mo("Kingella kingae"),
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PEN = "S",
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AMX = "-",
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stringsAsFactors = FALSE)
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, info = FALSE))$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"), info = TRUE)))
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# check verbose output
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expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
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# AmpC de-repressed cephalo mutants
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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ampc_cephalosporin_resistance = "R",
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info = FALSE)$cefotax,
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as.rsi(c("S", "R")))
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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ampc_cephalosporin_resistance = NA,
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info = FALSE)$cefotax,
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as.rsi(c("S", NA)))
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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ampc_cephalosporin_resistance = NULL,
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info = FALSE)$cefotax,
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as.rsi(c("S", "S")))
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# EUCAST dosage -----------------------------------------------------------
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expect_equal(nrow(eucast_dosage(c("tobra", "genta", "cipro"))), 3)
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expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
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})
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