AMR/inst/tinytest/test-rsi.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2022 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/   #
# ==================================================================== #

# we must only have EUCAST and CLSI, because otherwise the rules in as.rsi() will fail
expect_identical(unique(gsub("[^A-Z]", "", AMR::rsi_translation$guideline)),
                 c("EUCAST", "CLSI"))

expect_true(as.rsi("S") < as.rsi("I"))
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S")))
x <- example_isolates$AMX
expect_inherits(x[1], "rsi")
expect_inherits(x[[1]], "rsi")
expect_inherits(c(x[1], x[9]), "rsi")
expect_inherits(unique(x[1], x[9]), "rsi")
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_silent(plot(as.rsi(c("S", "I", "R"))))
if (AMR:::pkg_is_available("ggplot2")) {
  expect_inherits(autoplot(as.rsi(c("S", "I", "R"))), "gg")
}
expect_stdout(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
expect_equal(summary(as.rsi(c("S", "R"))),
             structure(c("Class" = "rsi",
                         "%R" = "50.0% (n=1)",
                         "%SI" = "50.0% (n=1)",
                         "- %S" = "50.0% (n=1)",
                         "- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
                 as.logical(lapply(example_isolates, is.rsi)))
expect_error(as.rsi.mic(as.mic(16)))
expect_error(as.rsi.disk(as.disk(16)))
expect_error(get_guideline("this one does not exist"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  # 40 rsi columns
  expect_equal(example_isolates %>%
                 mutate_at(vars(PEN:RIF), as.character) %>%
                 lapply(is.rsi.eligible) %>%
                 as.logical() %>%
                 sum(),
               40)
  expect_equal(sum(is.rsi(example_isolates)), 40)
  
  expect_stdout(print(tibble(ab = as.rsi("S"))))
}
if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
  expect_inherits(skim(example_isolates),
                  "data.frame")
  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
    expect_inherits(example_isolates %>%
                      mutate(m = as.mic(2),
                             d = as.disk(20)) %>% 
                      skim(),
                    "data.frame")
  }
}

expect_equal(as.rsi(c("", "-", NA, "NULL")), c(NA_rsi_, NA_rsi_, NA_rsi_, NA_rsi_))

# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(as.character(
  as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
         mo = "B_STRPT_PNMN",
         ab = "AMP",
         guideline = "EUCAST 2020")),
  c("S", "S", "I", "I", "R"))
# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
expect_equal(as.character(
  as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
         mo = "B_STRPT_PNMN",
         ab = "AMX",
         guideline = "CLSI 2019")),
  c("S", "S", "I", "R", "R"))

# cutoffs at MIC = 8
expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
             as.rsi("S"))
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
             as.rsi("R"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  expect_true(suppressWarnings(example_isolates %>%
                                 mutate(amox_mic = as.mic(2)) %>%
                                 select(mo, amox_mic) %>%
                                 as.rsi() %>%
                                 pull(amox_mic) %>%
                                 is.rsi()))
}

expect_equal(as.character(
  as.rsi(x = as.disk(22),
         mo = "B_STRPT_PNMN",
         ab = "ERY",
         guideline = "CLSI")),
  "S")
expect_equal(as.character(
  as.rsi(x = as.disk(18),
         mo = "B_STRPT_PNMN",
         ab = "ERY",
         guideline = "CLSI")),
  "I")
expect_equal(as.character(
  as.rsi(x = as.disk(10),
         mo = "B_STRPT_PNMN",
         ab = "ERY",
         guideline = "CLSI")),
  "R")
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  expect_true(example_isolates %>%
                mutate(amox_disk = as.disk(15)) %>%
                select(mo, amox_disk) %>%
                as.rsi(guideline = "CLSI") %>%
                pull(amox_disk) %>%
                is.rsi())
}
# frequency tables
if (AMR:::pkg_is_available("cleaner")) {
  expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
}


df <- data.frame(microorganism = "Escherichia coli",
                 AMP = as.mic(8),
                 CIP = as.mic(0.256),
                 GEN = as.disk(18),
                 TOB = as.disk(16),
                 ERY = "R", # note about assigning <rsi> class
                 CLR = "V") # note about cleaning
expect_inherits(suppressWarnings(as.rsi(df)),
                "data.frame")
expect_inherits(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
                                                   amoxi = c("R", "S", "I", "invalid")))$amoxi),
                "rsi")
expect_warning(as.rsi(data.frame(mo = "E. coli",
                                 NIT = c("<= 2", 32))))
expect_message(as.rsi(data.frame(mo = "E. coli",
                                 NIT = c("<= 2", 32),
                                 uti = TRUE)))
expect_message(as.rsi(data.frame(mo = "E. coli",
                                 NIT = c("<= 2", 32),
                                 specimen = c("urine", "blood"))))