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270 lines
12 KiB
R
270 lines
12 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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://amr-for-r.org #
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# ==================================================================== #
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test_that("test-antibiogram.R", {
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skip_on_cran()
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# 'I' follows the guideline, see section 'Interpretation of SIR' in ?as.sir
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get_gen <- function(...) suppressWarnings(antibiogram(example_isolates, antimicrobials = "GEN", ab_transform = NULL, formatting_type = 1, ...))$GEN
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gen_eucast <- get_gen(guideline = "EUCAST")
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gen_clsi <- get_gen(guideline = "CLSI")
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expect_true(all(gen_eucast >= gen_clsi, na.rm = TRUE) && any(gen_eucast > gen_clsi, na.rm = TRUE))
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expect_error(antibiogram(example_isolates, antimicrobials = "GEN", guideline = NULL))
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# the deprecated combine_SI must be followed literally if set, regardless of the guideline
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expect_identical(get_gen(combine_SI = TRUE, guideline = "CLSI"), gen_eucast)
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expect_identical(get_gen(combine_SI = FALSE, guideline = "EUCAST"), gen_clsi) # identical since example_isolates contains no SDD
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# isolates of unknown species must be included, also in WISCA
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set.seed(1)
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wisca_all <- suppressMessages(wisca(example_isolates, antimicrobials = "GEN", simulations = 100, info = FALSE, guideline = "EUCAST"))
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set.seed(1)
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wisca_known <- suppressMessages(wisca(example_isolates[example_isolates$mo != "UNKNOWN", ], antimicrobials = "GEN", simulations = 100, info = FALSE, guideline = "EUCAST"))
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expect_true("UNKNOWN" %in% attributes(wisca_all)$wisca_parameters$mo)
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expect_false(identical(as.data.frame(wisca_all), as.data.frame(wisca_known)))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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ab_grouped <- tryCatch(
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example_isolates %>% group_by(ward) %>% antibiogram(antimicrobials = "GEN", minimum = 0, formatting_type = 1, guideline = "EUCAST"),
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warning = function(w) conditionMessage(w)
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)
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expect_inherits(ab_grouped, "antibiogram")
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expect_true(mo_shortname("UNKNOWN", language = NULL) %in% ab_grouped[[2]])
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expect_false(any(as.character(ab_grouped[[2]]) %in% c("UNKNOWN", "B_ESCHR_COLI")))
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}
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# Traditional antibiogram ----------------------------------------------
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ab0 <- antibiogram(example_isolates)
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# the column names of ab1 to ab6 and ab8 to ab9 are tested in English, which must also hold on systems in another language
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ab1 <- antibiogram(example_isolates,
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antimicrobials = c(aminoglycosides(), carbapenems()),
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language = "en"
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)
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ab2 <- antibiogram(example_isolates,
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antimicrobials = aminoglycosides(),
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ab_transform = "atc",
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mo_transform = "gramstain",
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language = "en"
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)
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ab3 <- antibiogram(example_isolates,
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antimicrobials = carbapenems(),
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ab_transform = "ab",
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mo_transform = "name",
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formatting_type = 1,
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language = "en"
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)
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expect_inherits(ab1, "antibiogram")
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expect_inherits(ab2, "antibiogram")
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expect_inherits(ab3, "antibiogram")
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expect_equal(colnames(ab1), c("Pathogen", "Amikacin", "Gentamicin", "Imipenem", "Kanamycin", "Meropenem", "Tobramycin"))
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expect_equal(colnames(ab2), c("Pathogen", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
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expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM"))
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expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
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# Combined antibiogram -------------------------------------------------
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# combined antibiogram yield higher empiric coverage
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ab4 <- antibiogram(example_isolates,
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antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
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mo_transform = "gramstain",
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language = "en"
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)
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ab5 <- antibiogram(example_isolates,
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antimicrobials = c("TZP", "TZP+TOB"),
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mo_transform = "gramstain",
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ab_transform = "name",
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sep = " & ",
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add_total_n = FALSE,
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language = "en"
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)
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expect_inherits(ab4, "antibiogram")
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expect_inherits(ab5, "antibiogram")
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expect_equal(colnames(ab4), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
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expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam & Tobramycin"))
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# Syndromic antibiogram ------------------------------------------------
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# the data set could contain a filter for e.g. respiratory specimens
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ab6 <- antibiogram(example_isolates,
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antimicrobials = c(aminoglycosides(), carbapenems()),
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syndromic_group = "ward",
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ab_transform = NULL,
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language = "en"
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)
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# with a custom language, though this will be determined automatically
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# (i.e., this table will be in Dutch on Dutch systems)
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ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
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ab7 <- antibiogram(ex1,
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antimicrobials = aminoglycosides(),
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ab_transform = "name",
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syndromic_group = ifelse(ex1$ward == "ICU",
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"IC", "Geen IC"
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),
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language = "nl"
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)
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expect_inherits(ab6, "antibiogram")
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expect_inherits(ab7, "antibiogram")
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expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
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expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen", "Amikacine", "Gentamicine", "Tobramycine"))
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# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
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# the data set could contain a filter for e.g. respiratory specimens
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ab8 <- suppressWarnings(antibiogram(example_isolates,
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antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
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wisca = TRUE,
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language = "en"
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))
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expect_inherits(ab8, "antibiogram")
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expect_inherits(retrieve_wisca_parameters(ab8), "data.frame")
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expect_inherits(attributes(ab8)$long_numeric, "data.frame")
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expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
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# grouped tibbles
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_warning(
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ab9 <- example_isolates %>%
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group_by(ward, gender) %>%
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wisca(antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), language = "en")
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)
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expect_equal(colnames(ab9), c("ward", "gender", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
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}
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# Parallel computing ----------------------------------------------------
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# Tests must pass even when only 1 core is available; parallel = TRUE then
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# silently falls back to sequential, but results must still be correct.
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if (AMR:::pkg_is_available("future.apply")) {
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set.seed(42)
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# sequential reference for WISCA
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wisca_seq <- suppressWarnings(suppressMessages(
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wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, info = FALSE)
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))
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future::plan(future::multicore)
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# 1. parallel = TRUE produces the same antibiogram structure as sequential
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wisca_par <- suppressWarnings(suppressMessages(
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wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
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))
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expect_inherits(wisca_par, "antibiogram")
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expect_equal(colnames(wisca_par), colnames(wisca_seq))
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expect_true(isTRUE(attributes(wisca_par)$wisca))
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# 2. coverage values are non-NA and fall within [0, 1]
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ln <- attributes(wisca_par)$long_numeric
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expect_false(anyNA(ln$coverage))
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expect_false(anyNA(ln$lower_ci))
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expect_false(anyNA(ln$upper_ci))
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expect_true(all(ln$coverage >= 0 & ln$coverage <= 1))
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expect_true(all(ln$lower_ci <= ln$coverage))
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expect_true(all(ln$upper_ci >= ln$coverage))
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# 3. a second parallel run gives the same column names
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wisca_par2 <- suppressWarnings(suppressMessages(
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wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
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))
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expect_equal(colnames(wisca_par), colnames(wisca_par2))
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# 4. parallel with workers = 1 gives same structure as sequential
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future::plan(future::multicore, workers = 1)
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wisca_par1 <- suppressWarnings(suppressMessages(
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wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
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))
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expect_equal(colnames(wisca_seq), colnames(wisca_par1))
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# 5. grouped antibiogram in parallel yields identical structure to sequential
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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future::plan(future::sequential)
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ab_grp_seq <- suppressWarnings(suppressMessages(
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example_isolates %>%
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group_by(ward) %>%
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wisca(antimicrobials = c("TZP", "TZP+TOB"), simulations = 50, info = FALSE)
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))
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future::plan(future::multicore)
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ab_grp_par <- suppressWarnings(suppressMessages(
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example_isolates %>%
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group_by(ward) %>%
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wisca(antimicrobials = c("TZP", "TZP+TOB"), simulations = 50, parallel = TRUE, info = FALSE)
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))
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expect_equal(colnames(ab_grp_seq), colnames(ab_grp_par))
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expect_equal(nrow(ab_grp_seq), nrow(ab_grp_par))
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}
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# 6. parallel = TRUE without a plan raises an informative error
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future::plan(future::sequential)
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expect_error(
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suppressWarnings(wisca(example_isolates, antimicrobials = "TZP", parallel = TRUE, info = FALSE)),
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"non-sequential"
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)
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future::plan(future::sequential)
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}
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# Generate plots with ggplot2 or base R --------------------------------
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(plot(ab1))
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expect_silent(plot(ab2))
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expect_silent(plot(ab3))
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expect_silent(plot(ab4))
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expect_silent(plot(ab5))
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expect_silent(plot(ab6))
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expect_silent(plot(ab7))
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expect_silent(plot(ab8))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_silent(plot(ab9))
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}
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(ggplot2::autoplot(ab1), "gg")
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expect_inherits(ggplot2::autoplot(ab2), "gg")
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expect_inherits(ggplot2::autoplot(ab3), "gg")
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expect_inherits(ggplot2::autoplot(ab4), "gg")
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expect_inherits(ggplot2::autoplot(ab5), "gg")
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expect_inherits(ggplot2::autoplot(ab6), "gg")
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expect_inherits(ggplot2::autoplot(ab7), "gg")
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expect_inherits(ggplot2::autoplot(ab8), "gg")
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_inherits(ggplot2::autoplot(ab9), "gg")
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}
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}
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})
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