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(v2.1.1.9186) replace antibiotics with antimicrobials!
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@ -27,130 +27,131 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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test_that("antibiogram works", {
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# Traditional antibiogram ----------------------------------------------
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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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)
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ab1 <- antibiogram(example_isolates,
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antibiotics = c(aminoglycosides(), carbapenems())
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)
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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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add_total_n = TRUE
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)
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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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add_total_n = TRUE
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)
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ab3 <- antibiogram(example_isolates,
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antibiotics = 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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)
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ab3 <- antibiogram(example_isolates,
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antibiotics = 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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)
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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 (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
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expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM"))
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expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
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expect_inherits(ab1, "antibiogram")
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expect_inherits(ab2, "antibiogram")
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expect_inherits(ab3, "antibiogram")
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expect_equal(colnames(ab1), c("Pathogen", "Amikacin", "Gentamicin", "Imipenem", "Kanamycin", "Meropenem", "Tobramycin"))
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expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
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expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM"))
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expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
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# Combined antibiogram -------------------------------------------------
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# Combined antibiogram -------------------------------------------------
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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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)
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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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)
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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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)
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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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)
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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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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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# 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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ab_transform = NULL
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)
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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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ab_transform = NULL
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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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antibiotics = aminoglycosides(),
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ab_transform = "name",
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syndromic_group = ifelse(ex1$ward == "ICU",
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"IC", "Geen IC"
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),
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language = "nl",
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add_total_n = TRUE
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)
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# with a custom language, though this will be determined automatically
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# (i.e., this table will be in Dutch on Dutch systems)
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ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
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ab7 <- antibiogram(ex1,
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antibiotics = aminoglycosides(),
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ab_transform = "name",
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syndromic_group = ifelse(ex1$ward == "ICU",
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"IC", "Geen IC"
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),
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language = "nl",
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add_total_n = TRUE
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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 (N min-max)", "Amikacine", "Gentamicine", "Tobramycine"))
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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 (N min-max)", "Amikacine", "Gentamicine", "Tobramycine"))
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# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
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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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antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
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wisca = TRUE
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))
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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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antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
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wisca = TRUE
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))
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expect_inherits(ab8, "antibiogram")
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expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
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expect_inherits(ab8, "antibiogram")
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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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# grouped tibbles
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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ab9 <- example_isolates %>%
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group_by(ward, gender) %>%
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wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
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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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# 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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ab9 <- example_isolates %>%
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group_by(ward, gender) %>%
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wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
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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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}
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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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