# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # context("eucast_rules.R") test_that("EUCAST rules work", { skip_on_cran() # thoroughly check input table expect_equal(colnames(eucast_rules_file), c("if_mo_property", "like.is.one_of", "this_value", "and_these_antibiotics", "have_these_values", "then_change_these_antibiotics", "to_value", "reference.rule", "reference.rule_group", "reference.version", "note")) MOs_mentioned <- unique(eucast_rules_file$this_value) MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_valid_regex(MOs_mentioned)], ",", fixed = TRUE)))) MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned))) expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0) expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing"))) expect_error(eucast_rules(x = "text")) expect_error(eucast_rules(data.frame(a = "test"))) expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set")) expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE))) expect_identical(colnames(example_isolates), colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE)))) expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE))) a <- data.frame(mo = c("Klebsiella pneumoniae", "Pseudomonas aeruginosa", "Enterobacter cloacae"), amox = "-", # Amoxicillin stringsAsFactors = FALSE) b <- data.frame(mo = c("Klebsiella pneumoniae", "Pseudomonas aeruginosa", "Enterobacter cloacae"), amox = "R", # Amoxicillin stringsAsFactors = FALSE) expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b) expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE)))) a <- data.frame(mo = c("Staphylococcus aureus", "Streptococcus group A"), COL = "-", # Colistin stringsAsFactors = FALSE) b <- data.frame(mo = c("Staphylococcus aureus", "Streptococcus group A"), COL = "R", # Colistin stringsAsFactors = FALSE) expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b) # piperacillin must be R in Enterobacteriaceae when tica is R if (suppressWarnings(require("dplyr"))) { expect_equal(suppressWarnings( example_isolates %>% filter(mo_family(mo) == "Enterobacteriaceae") %>% mutate(TIC = as.rsi("R"), PIP = as.rsi("S")) %>% eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>% pull(PIP) %>% unique() %>% as.character()), "R") } # Azithromycin and Clarythromycin must be equal to Erythromycin a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo, ERY = example_isolates$ERY, AZM = as.rsi("R"), CLR = factor("R"), stringsAsFactors = FALSE), version_expertrules = 3.1, only_rsi_columns = FALSE)$CLR)) b <- example_isolates$ERY expect_identical(a[!is.na(b)], b[!is.na(b)]) # amox is inferred by benzylpenicillin in Kingella kingae expect_equal( suppressWarnings( as.list(eucast_rules( data.frame(mo = as.mo("Kingella kingae"), PEN = "S", AMX = "-", stringsAsFactors = FALSE) , info = FALSE))$AMX ), "S") # also test norf if (suppressWarnings(require("dplyr"))) { expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE))) } # check verbose output expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE))) # AmpC de-repressed cephalo mutants expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), ampc_cephalosporin_resistance = TRUE, info = FALSE)$cefotax, as.rsi(c("S", "R"))) expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), ampc_cephalosporin_resistance = NA, info = FALSE)$cefotax, as.rsi(c("S", NA))) expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), ampc_cephalosporin_resistance = NULL, info = FALSE)$cefotax, as.rsi(c("S", "S"))) # EUCAST dosage ----------------------------------------------------------- expect_equal(nrow(eucast_dosage(c("tobra", "genta", "cipro"))), 3) expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame") }) test_that("Custom EUCAST rules work", { skip_on_cran() x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I", AMX == "S" ~ AMC == "S") expect_output(print(x)) expect_output(print(c(x, x))) expect_output(print(as.list(x, x))) # this custom rules makes 8 changes expect_equal(nrow(eucast_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE, verbose = TRUE)), 8) })