AMR/inst/tinytest/test-eucast_rules.R

# ==================================================================== #
# 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/   #
# ==================================================================== #

# thoroughly check input table
expect_equal(colnames(AMR:::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(AMR:::eucast_rules_file$this_value)
MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_true(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_stdout(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_stdout(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 (AMR:::pkg_is_available("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 (AMR:::pkg_is_available("dplyr")) {
  expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}

# check verbose output
expect_stdout(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_inherits(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")



x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
                         AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I",
                         AMX == "S" ~ AMC == "S")
expect_stdout(print(x))
expect_stdout(print(c(x, x)))
expect_stdout(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, tolerance = 0.5)