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revert back to pre-antibiogram
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@ -1,132 +0,0 @@
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# ==================================================================== #
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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 #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi: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://msberends.github.io/AMR/ #
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# ==================================================================== #
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# Traditional antibiogram ----------------------------------------------
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ab1 <- antibiogram(example_isolates,
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antibiotics = c(aminoglycosides(), carbapenems()))
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ab2 <- antibiogram(example_isolates,
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antibiotics = aminoglycosides(),
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ab_transform = "atc",
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mo_transform = "gramstain")
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ab3 <- antibiogram(example_isolates,
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antibiotics = carbapenems(),
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ab_transform = "name",
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mo_transform = "name")
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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 (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
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expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
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expect_equal(colnames(ab3), c("Pathogen (N min-max)", "Imipenem", "Meropenem"))
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expect_equal(ab3$Meropenem, c(52, NA, 100, 100, NA))
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# Combined antibiogram -------------------------------------------------
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# combined antibiotics yield higher empiric coverage
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ab4 <- antibiogram(example_isolates,
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antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
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mo_transform = "gramstain")
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ab5 <- antibiogram(example_isolates,
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antibiotics = 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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expect_inherits(ab4, "antibiogram")
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expect_inherits(ab5, "antibiogram")
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expect_equal(colnames(ab4), c("Pathogen (N min-max)", "TZP", "TZP + GEN", "TZP + TOB"))
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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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antibiotics = c(aminoglycosides(), carbapenems()),
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syndromic_group = "ward")
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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 Spanish on Spanish systems)
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ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
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ab7 <- antibiogram(ex1,
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antibiotics = aminoglycosides(),
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ab_transform = "name",
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syndromic_group = ifelse(ex1$ward == "ICU",
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"UCI", "No UCI"),
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language = "es")
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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 (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
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expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
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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 <- antibiogram(example_isolates,
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antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
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mo_transform = "gramstain",
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minimum = 10, # this should be >= 30, but now just as example
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syndromic_group = ifelse(example_isolates$age >= 65 &
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example_isolates$gender == "M",
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"WISCA Group 1", "WISCA Group 2"))
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expect_inherits(ab8, "antibiogram")
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expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen (N min-max)", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
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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("ggplot2")) {
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expect_inherits(autoplot(ab1), "gg")
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expect_inherits(autoplot(ab2), "gg")
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expect_inherits(autoplot(ab3), "gg")
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expect_inherits(autoplot(ab4), "gg")
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expect_inherits(autoplot(ab5), "gg")
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expect_inherits(autoplot(ab6), "gg")
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expect_inherits(autoplot(ab7), "gg")
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expect_inherits(autoplot(ab8), "gg")
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}
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@ -228,7 +228,7 @@ expect_identical(
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# notice that all mo's are distinct, so all are TRUE
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expect_true(all(first_isolate(AMR:::distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE))
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expect_true(all(first_isolate(AMR:::pm_distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE))
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# only one isolate, so return fast
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expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
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@ -32,21 +32,11 @@
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# functions used by import_fn()
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import_functions <- c(
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"%>%" = "dplyr",
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"%chin%" = "data.table",
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"across" = "dplyr",
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"anti_join" = "dplyr",
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"arrange" = "dplyr",
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"bind_rows" = "dplyr",
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"chmatch" = "data.table",
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"count" = "dplyr",
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"cur_column" = "dplyr",
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"desc" = "dplyr",
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"distinct" = "dplyr",
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"everything" = "dplyr",
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"full_join" = "dplyr",
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"group_by" = "dplyr",
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"group_vars" = "dplyr",
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"has_internet" = "curl",
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"html_attr" = "rvest",
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"html_children" = "rvest",
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@ -56,24 +46,13 @@ import_functions <- c(
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"html_text" = "rvest",
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"inner_join" = "dplyr",
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"insertText" = "rstudioapi",
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"kable" = "knitr",
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"lag" = "dplyr",
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"left_join" = "dplyr",
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"mutate" = "dplyr",
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"n_distinct" = "dplyr",
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"new_pillar_shaft_simple" = "pillar",
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"pivot_longer" = "tidyr",
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"progress_bar" = "progress",
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"pull" = "dplyr",
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"read_html" = "xml2",
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"rename" = "dplyr",
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"right_join" = "dplyr",
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"select" = "dplyr",
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"semi_join" = "dplyr",
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"showQuestion" = "rstudioapi",
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"summarise" = "dplyr",
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"ungroup" = "dplyr",
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"where" = "dplyr"
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"showQuestion" = "rstudioapi"
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)
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# functions that are called directly with ::
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@ -92,7 +71,6 @@ call_functions <- c(
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"element_text" = "ggplot2",
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"expand_limits" = "ggplot2",
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"facet_wrap" = "ggplot2",
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"geom_col" = "ggplot2",
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"geom_errorbar" = "ggplot2",
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"geom_path" = "ggplot2",
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"geom_point" = "ggplot2",
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@ -137,7 +115,7 @@ for (i in seq_len(length(import_functions))) {
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# function should exist in foreign pkg namespace
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if (AMR:::pkg_is_available(pkg,
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also_load = FALSE,
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min_version = if (pkg %in% c("dplyr", "tidyr")) "1.0.0" else NULL
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min_version = if (pkg == "dplyr") "1.0.0" else NULL
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)) {
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tst <- !is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE))
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expect_true(tst,
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