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(v2.1.1.9078) 12 new formatting formats for antibiogram(), prepare for Bayesian WISCA

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dr. M.S. (Matthijs) Berends
2024-09-22 11:45:51 +02:00
parent 28bf91cbf5
commit 127892430d
8 changed files with 201 additions and 61 deletions
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29
inst/tinytest/test-antibiogram.R
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@ -36,20 +36,22 @@ ab1 <- antibiogram(example_isolates,
ab2 <- antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain")
mo_transform = "gramstain",
add_total_n = TRUE)
ab3 <- antibiogram(example_isolates,
antibiotics = carbapenems(),
ab_transform = "name",
mo_transform = "name")
ab_transform = "ab",
mo_transform = "name",
formatting_type = 1)
expect_inherits(ab1, "antibiogram")
expect_inherits(ab2, "antibiogram")
expect_inherits(ab3, "antibiogram")
expect_equal(colnames(ab1), c("Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab1), c("Pathogen", "Amikacin", "Gentamicin", "Imipenem", "Kanamycin", "Meropenem", "Tobramycin"))
expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
expect_equal(colnames(ab3), c("Pathogen (N min-max)", "Imipenem", "Meropenem"))
expect_equal(ab3$Meropenem, c(52, NA, 100, 100, NA))
expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM"))
expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
# Combined antibiogram -------------------------------------------------
@ -67,7 +69,7 @@ ab5 <- antibiogram(example_isolates,
expect_inherits(ab4, "antibiogram")
expect_inherits(ab5, "antibiogram")
expect_equal(colnames(ab4), c("Pathogen (N min-max)", "TZP", "TZP + GEN", "TZP + TOB"))
expect_equal(colnames(ab4), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam & Tobramycin"))
# Syndromic antibiogram ------------------------------------------------
@ -75,7 +77,8 @@ expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacill
# the data set could contain a filter for e.g. respiratory specimens
ab6 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
syndromic_group = "ward",
ab_transform = NULL)
# with a custom language, though this will be determined automatically
# (i.e., this table will be in Dutch on Dutch systems)
@ -85,11 +88,12 @@ ab7 <- antibiogram(ex1,
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"IC", "Geen IC"),
language = "nl")
language = "nl",
add_total_n = TRUE)
expect_inherits(ab6, "antibiogram")
expect_inherits(ab7, "antibiogram")
expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikacine", "Gentamicine", "Tobramycine"))
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
@ -101,10 +105,11 @@ ab8 <- antibiogram(example_isolates,
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
"WISCA Group 1", "WISCA Group 2"),
ab_transform = NULL)
expect_inherits(ab8, "antibiogram")
expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen (N min-max)", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
# Generate plots with ggplot2 or base R --------------------------------