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(v2.1.1.9163) cleanup
This commit is contained in:
@ -80,15 +80,19 @@ expect_equal(
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# based on Levenshtein distance
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expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
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expect_identical(as.character(as.ab(c("gentamicine High Level",
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"gentamicine High",
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"gentamicine (High Level)",
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"gentamicine (High)",
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"gentamicine HL",
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"gentamicine H-L",
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"gentamicine (HL)",
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"gentamicine (H-L)"))),
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rep("GEH", 8))
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expect_identical(
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as.character(as.ab(c(
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"gentamicine High Level",
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"gentamicine High",
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"gentamicine (High Level)",
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"gentamicine (High)",
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"gentamicine HL",
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"gentamicine H-L",
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"gentamicine (HL)",
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"gentamicine (H-L)"
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))),
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rep("GEH", 8)
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)
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# assigning and subsetting
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x <- antibiotics$ab
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@ -96,4 +96,3 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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set_ab_names(NIT:VAN) %>%
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colnames())))
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}
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@ -35,13 +35,14 @@ expect_equal(
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c(39, 34, 29)
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)
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expect_equal(age(
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x = c("2019-01-01", "2019-04-01", "2019-07-01"),
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reference = "2019-09-01",
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exact = TRUE
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),
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c(0.6656393, 0.4191781, 0.1698630),
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tolerance = 0.001
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expect_equal(
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age(
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x = c("2019-01-01", "2019-04-01", "2019-07-01"),
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reference = "2019-09-01",
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exact = TRUE
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),
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c(0.6656393, 0.4191781, 0.1698630),
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tolerance = 0.001
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)
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expect_error(age(
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@ -31,19 +31,22 @@
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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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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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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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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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@ -57,15 +60,17 @@ expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
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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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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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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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@ -76,20 +81,23 @@ expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacill
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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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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$ward == "ICU",
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"IC", "Geen IC"),
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language = "nl",
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add_total_n = TRUE)
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antibiotics = aminoglycosides(),
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ab_transform = "name",
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syndromic_group = ifelse(ex1$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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@ -100,8 +108,9 @@ expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikaci
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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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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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@ -34,7 +34,7 @@ expect_identical(av_cid("ACI"), as.integer(135398513))
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expect_inherits(av_tradenames("ACI"), "character")
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expect_inherits(av_tradenames(c("ACI", "ACI")), "list")
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expect_identical(av_group("ACI", language = NULL),"Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
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expect_identical(av_group("ACI", language = NULL), "Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
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expect_identical(av_name(135398513, language = NULL), "Aciclovir")
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expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
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@ -69,7 +69,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
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example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)
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)
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# count of cases
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expect_equal(
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example_isolates %>%
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@ -33,9 +33,11 @@ expect_message(as.ab("testab", info = TRUE))
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suppressMessages(
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add_custom_antimicrobials(
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data.frame(ab = "TESTAB",
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name = "Test Antibiotic",
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group = "Test Group")
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data.frame(
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ab = "TESTAB",
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name = "Test Antibiotic",
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group = "Test Group"
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)
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)
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)
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@ -27,14 +27,18 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(as.mo("Enterobacter asburiae/cloacae"),
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as.mo("Enterobacter asburiae"))
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expect_identical(
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as.mo("Enterobacter asburiae/cloacae"),
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as.mo("Enterobacter asburiae")
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)
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suppressMessages(
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add_custom_microorganisms(
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data.frame(mo = "ENT_ASB_CLO",
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genus = "Enterobacter",
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species = "asburiae/cloacae")
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data.frame(
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mo = "ENT_ASB_CLO",
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genus = "Enterobacter",
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species = "asburiae/cloacae"
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)
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)
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)
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@ -44,8 +48,12 @@ expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
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if (getRversion() >= "3.3.0") {
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# until R 3.2, abbreviate() used a completely different algorithm, making these tests unreproducible
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expect_identical(paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
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as.character(as.mo("Klebsiella pneumoniae")))
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expect_identical(paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
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as.character(as.mo("Aerococcus urinae")))
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expect_identical(
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paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
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as.character(as.mo("Klebsiella pneumoniae"))
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)
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expect_identical(
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paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
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as.character(as.mo("Aerococcus urinae"))
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)
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}
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@ -68,9 +68,9 @@ if (AMR:::pkg_is_available("tibble")) {
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df <- AMR:::AMR_env$MO_lookup
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expect_true(all(c(
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"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies", "rank", "ref", "source",
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"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
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"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies", "rank", "ref", "source",
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"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
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"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
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) %in% colnames(df)))
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@ -117,15 +117,16 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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}
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# azithromycin and clarythromycin must be equal to Erythromycin
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a <- suppressWarnings(as.sir(eucast_rules(data.frame(
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mo = example_isolates$mo,
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ERY = example_isolates$ERY,
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AZM = as.sir("R"),
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CLR = factor("R"),
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stringsAsFactors = FALSE
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),
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version_expertrules = 3.1,
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only_sir_columns = FALSE
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a <- suppressWarnings(as.sir(eucast_rules(
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data.frame(
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mo = example_isolates$mo,
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ERY = example_isolates$ERY,
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AZM = as.sir("R"),
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CLR = factor("R"),
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stringsAsFactors = FALSE
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),
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version_expertrules = 3.1,
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only_sir_columns = FALSE
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)$CLR))
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b <- example_isolates$ERY
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expect_identical(
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@ -160,34 +161,37 @@ expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, ru
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# AmpC de-repressed cephalo mutants
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expect_identical(
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eucast_rules(data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = TRUE,
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info = FALSE
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eucast_rules(
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data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = TRUE,
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info = FALSE
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)$cefotax,
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as.sir(c("S", "R"))
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)
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expect_identical(
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eucast_rules(data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = NA,
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info = FALSE
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eucast_rules(
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data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = NA,
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info = FALSE
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)$cefotax,
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as.sir(c("S", NA))
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)
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expect_identical(
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eucast_rules(data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = NULL,
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info = FALSE
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eucast_rules(
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data.frame(
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mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.sir(c("S", "S"))
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),
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ampc_cephalosporin_resistance = NULL,
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info = FALSE
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)$cefotax,
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as.sir(c("S", "S"))
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)
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@ -208,12 +212,13 @@ expect_stdout(print(c(x, x)))
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expect_stdout(print(as.list(x, x)))
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# this custom rules makes 8 changes
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expect_equal(nrow(eucast_rules(example_isolates,
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rules = "custom",
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custom_rules = x,
|
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info = FALSE,
|
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verbose = TRUE
|
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)),
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8,
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tolerance = 0.5
|
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expect_equal(
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nrow(eucast_rules(example_isolates,
|
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rules = "custom",
|
||||
custom_rules = x,
|
||||
info = FALSE,
|
||||
verbose = TRUE
|
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)),
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||||
8,
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tolerance = 0.5
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||||
)
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@ -46,17 +46,28 @@ expect_equal(
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)
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# for phenotype determination
|
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expect_equal(AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
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FALSE)
|
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expect_equal(AMR:::duplicated_antibiogram(c("RRR", "SSS"),
|
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points_threshold = 2, ignore_I = TRUE, type = "points"),
|
||||
c(FALSE, FALSE))
|
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expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
|
||||
points_threshold = 2, ignore_I = TRUE, type = "points"),
|
||||
c(FALSE, TRUE, FALSE))
|
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expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
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||||
points_threshold = 2, ignore_I = TRUE, type = "points"),
|
||||
c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE))
|
||||
expect_equal(
|
||||
AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
|
||||
FALSE
|
||||
)
|
||||
expect_equal(
|
||||
AMR:::duplicated_antibiogram(c("RRR", "SSS"),
|
||||
points_threshold = 2, ignore_I = TRUE, type = "points"
|
||||
),
|
||||
c(FALSE, FALSE)
|
||||
)
|
||||
expect_equal(
|
||||
AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
|
||||
points_threshold = 2, ignore_I = TRUE, type = "points"
|
||||
),
|
||||
c(FALSE, TRUE, FALSE)
|
||||
)
|
||||
expect_equal(
|
||||
AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
|
||||
points_threshold = 2, ignore_I = TRUE, type = "points"
|
||||
),
|
||||
c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)
|
||||
)
|
||||
|
||||
# Phenotype-based, using key antimicrobials
|
||||
expect_equal(
|
||||
@ -89,7 +100,9 @@ expect_true(
|
||||
col_icu = example_isolates$ward == "ICU",
|
||||
info = TRUE,
|
||||
icu_exclude = TRUE
|
||||
), na.rm = TRUE) < 950
|
||||
),
|
||||
na.rm = TRUE
|
||||
) < 950
|
||||
)
|
||||
|
||||
# set 1500 random observations to be of specimen type 'Urine'
|
||||
|
||||
@ -28,7 +28,7 @@
|
||||
# ==================================================================== #
|
||||
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
|
||||
AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
|
||||
AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
|
||||
pdf(NULL) # prevent Rplots.pdf being created
|
||||
|
||||
# data should be equal
|
||||
@ -43,15 +43,19 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
|
||||
summarise_all(resistance) %>%
|
||||
as.double()
|
||||
)
|
||||
|
||||
expect_inherits(example_isolates %>%
|
||||
select(AMC, CIP) %>%
|
||||
ggplot_sir(x = "interpretation", facet = "antibiotic"),
|
||||
"gg")
|
||||
expect_inherits(example_isolates %>%
|
||||
select(AMC, CIP) %>%
|
||||
ggplot_sir(x = "antibiotic", facet = "interpretation"),
|
||||
"gg")
|
||||
|
||||
expect_inherits(
|
||||
example_isolates %>%
|
||||
select(AMC, CIP) %>%
|
||||
ggplot_sir(x = "interpretation", facet = "antibiotic"),
|
||||
"gg"
|
||||
)
|
||||
expect_inherits(
|
||||
example_isolates %>%
|
||||
select(AMC, CIP) %>%
|
||||
ggplot_sir(x = "antibiotic", facet = "interpretation"),
|
||||
"gg"
|
||||
)
|
||||
|
||||
expect_equal(
|
||||
(example_isolates %>%
|
||||
|
||||
@ -55,36 +55,38 @@ expect_equal(
|
||||
|
||||
# test Dutch P. aeruginosa MDRO
|
||||
expect_equal(
|
||||
as.character(mdro(data.frame(
|
||||
mo = as.mo("P. aeruginosa"),
|
||||
cfta = "S",
|
||||
cipr = "S",
|
||||
mero = "S",
|
||||
imip = "S",
|
||||
gent = "S",
|
||||
tobr = "S",
|
||||
pita = "S"
|
||||
),
|
||||
guideline = "BRMO",
|
||||
col_mo = "mo",
|
||||
info = FALSE
|
||||
as.character(mdro(
|
||||
data.frame(
|
||||
mo = as.mo("P. aeruginosa"),
|
||||
cfta = "S",
|
||||
cipr = "S",
|
||||
mero = "S",
|
||||
imip = "S",
|
||||
gent = "S",
|
||||
tobr = "S",
|
||||
pita = "S"
|
||||
),
|
||||
guideline = "BRMO",
|
||||
col_mo = "mo",
|
||||
info = FALSE
|
||||
)),
|
||||
"Negative"
|
||||
)
|
||||
expect_equal(
|
||||
as.character(mdro(data.frame(
|
||||
mo = as.mo("P. aeruginosa"),
|
||||
cefta = "R",
|
||||
cipr = "R",
|
||||
mero = "R",
|
||||
imip = "R",
|
||||
gent = "R",
|
||||
tobr = "R",
|
||||
pita = "R"
|
||||
),
|
||||
guideline = "BRMO",
|
||||
col_mo = "mo",
|
||||
info = FALSE
|
||||
as.character(mdro(
|
||||
data.frame(
|
||||
mo = as.mo("P. aeruginosa"),
|
||||
cefta = "R",
|
||||
cipr = "R",
|
||||
mero = "R",
|
||||
imip = "R",
|
||||
gent = "R",
|
||||
tobr = "R",
|
||||
pita = "R"
|
||||
),
|
||||
guideline = "BRMO",
|
||||
col_mo = "mo",
|
||||
info = FALSE
|
||||
)),
|
||||
"Positive"
|
||||
)
|
||||
|
||||
@ -176,4 +176,3 @@ expect_true(as.mic("32") <= as.mic(32))
|
||||
expect_false(as.mic("32") <= as.mic("<32"))
|
||||
expect_true(as.mic("32") <= as.mic("<=32"))
|
||||
expect_false(as.mic("32") < as.mic("<=32"))
|
||||
|
||||
|
||||
@ -78,8 +78,10 @@ current_grampos_classes <- c(
|
||||
"Thermoleophilia",
|
||||
"Thermolithobacteria"
|
||||
)
|
||||
expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
|
||||
current_grampos_classes)
|
||||
expect_identical(
|
||||
sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
|
||||
current_grampos_classes
|
||||
)
|
||||
|
||||
expect_equal(mo_species("Escherichia coli"), "coli")
|
||||
expect_equal(mo_subspecies("Escherichia coli"), "")
|
||||
@ -103,11 +105,15 @@ expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
|
||||
expect_true(length(mo_group_members("B_HACEK")) > 1)
|
||||
expect_inherits(mo_group_members(c("Candida albicans", "Escherichia coli")), "list")
|
||||
|
||||
expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
|
||||
c("facultative anaerobe", "anaerobe"))
|
||||
expect_identical(
|
||||
mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
|
||||
c("facultative anaerobe", "anaerobe")
|
||||
)
|
||||
|
||||
expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
|
||||
c("1911", "72", "1", "16"))
|
||||
expect_equal(
|
||||
as.character(table(mo_pathogenicity(example_isolates$mo))),
|
||||
c("1911", "72", "1", "16")
|
||||
)
|
||||
|
||||
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
|
||||
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
|
||||
@ -118,8 +124,10 @@ expect_true(mo_url("Candida albicans") %like% "mycobank.org")
|
||||
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
|
||||
|
||||
# test integrity of getting back full names
|
||||
expect_identical(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
|
||||
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE)))
|
||||
expect_identical(
|
||||
microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
|
||||
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE))
|
||||
)
|
||||
|
||||
# check languages
|
||||
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
|
||||
@ -169,8 +177,10 @@ expect_identical(
|
||||
|
||||
expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
|
||||
expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
|
||||
expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
|
||||
c("Shimwellia blattae", "Escherichia coli"))
|
||||
expect_identical(
|
||||
mo_current(c("Escherichia blattae", "Escherichia coli")),
|
||||
c("Shimwellia blattae", "Escherichia coli")
|
||||
)
|
||||
|
||||
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
|
||||
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
|
||||
|
||||
@ -27,25 +27,27 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
resistance_data <- structure(list(
|
||||
order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
|
||||
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
|
||||
AMC = c(0.00425, 0.13062, 0.10344),
|
||||
CXM = c(0.00425, 0.05376, 0.10344),
|
||||
CTX = c(0.00000, 0.02396, 0.05172),
|
||||
TOB = c(0.02325, 0.02597, 0.10344),
|
||||
TMP = c(0.08387, 0.39141, 0.18367)
|
||||
),
|
||||
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
|
||||
row.names = c(NA, -3L),
|
||||
groups = structure(list(
|
||||
order = c("Bacillales", "Enterobacterales"),
|
||||
.rows = list(1L, 2:3)
|
||||
),
|
||||
row.names = c(NA, -2L),
|
||||
class = c("tbl_df", "tbl", "data.frame"),
|
||||
.drop = TRUE
|
||||
)
|
||||
resistance_data <- structure(
|
||||
list(
|
||||
order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
|
||||
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
|
||||
AMC = c(0.00425, 0.13062, 0.10344),
|
||||
CXM = c(0.00425, 0.05376, 0.10344),
|
||||
CTX = c(0.00000, 0.02396, 0.05172),
|
||||
TOB = c(0.02325, 0.02597, 0.10344),
|
||||
TMP = c(0.08387, 0.39141, 0.18367)
|
||||
),
|
||||
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
|
||||
row.names = c(NA, -3L),
|
||||
groups = structure(
|
||||
list(
|
||||
order = c("Bacillales", "Enterobacterales"),
|
||||
.rows = list(1L, 2:3)
|
||||
),
|
||||
row.names = c(NA, -2L),
|
||||
class = c("tbl_df", "tbl", "data.frame"),
|
||||
.drop = TRUE
|
||||
)
|
||||
)
|
||||
pca_model <- pca(resistance_data)
|
||||
expect_inherits(pca_model, "pca")
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
|
||||
pdf(NULL) # prevent Rplots.pdf being created
|
||||
|
||||
|
||||
# scale_*_mic
|
||||
aesthetics <- c("x", "y", "colour", "fill")
|
||||
expected_methods <- c("transform", "transform_df", "breaks", "labels", "limits")
|
||||
@ -38,10 +38,11 @@ if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
|
||||
scale_obj <- getExportedValue("ggplot2", scale_fn_name)()
|
||||
for (method in expected_methods) {
|
||||
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name))
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
# scale_*_sir
|
||||
aesthetics <- c("colour", "fill")
|
||||
expected_methods <- c("transform", "transform_df", "labels", "limits")
|
||||
@ -50,38 +51,64 @@ if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
|
||||
scale_obj <- getExportedValue("ggplot2", scale_fn_name)(aesthetics = aest)
|
||||
for (method in expected_methods) {
|
||||
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name))
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
|
||||
)
|
||||
}
|
||||
}
|
||||
for (method in expected_methods) {
|
||||
expect_true(is.function(ggplot2::scale_x_discrete()[[method]]) || method %in% names(ggplot2::scale_x_discrete()),
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete"))
|
||||
info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete")
|
||||
)
|
||||
}
|
||||
|
||||
expect_inherits(ggplot(data.frame(count = c(1,2,3, 4),
|
||||
sir = c("S", "I", "R", "SDD")),
|
||||
aes(x = sir, y = count, fill = sir)) +
|
||||
geom_col() +
|
||||
scale_x_sir(eucast_I = F, language = "el") +
|
||||
scale_fill_sir(eucast_I = T, language = "nl"),
|
||||
"gg")
|
||||
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))),
|
||||
aes(x = sir, y = mic)) +
|
||||
geom_point() +
|
||||
scale_y_mic(),
|
||||
"gg")
|
||||
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))),
|
||||
aes(x = sir, y = mic)) +
|
||||
geom_col() +
|
||||
scale_y_mic(),
|
||||
"gg")
|
||||
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))),
|
||||
aes(x = sir, y = mic)) +
|
||||
geom_col() +
|
||||
scale_y_mic(mic_range = c(4,16)) +
|
||||
scale_x_sir(),
|
||||
"gg")
|
||||
|
||||
expect_inherits(
|
||||
ggplot(
|
||||
data.frame(
|
||||
count = c(1, 2, 3, 4),
|
||||
sir = c("S", "I", "R", "SDD")
|
||||
),
|
||||
aes(x = sir, y = count, fill = sir)
|
||||
) +
|
||||
geom_col() +
|
||||
scale_x_sir(eucast_I = F, language = "el") +
|
||||
scale_fill_sir(eucast_I = T, language = "nl"),
|
||||
"gg"
|
||||
)
|
||||
expect_inherits(
|
||||
ggplot(
|
||||
data.frame(
|
||||
mic = as.mic(c(2, 4, 8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))
|
||||
),
|
||||
aes(x = sir, y = mic)
|
||||
) +
|
||||
geom_point() +
|
||||
scale_y_mic(),
|
||||
"gg"
|
||||
)
|
||||
expect_inherits(
|
||||
ggplot(
|
||||
data.frame(
|
||||
mic = as.mic(c(2, 4, 8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))
|
||||
),
|
||||
aes(x = sir, y = mic)
|
||||
) +
|
||||
geom_col() +
|
||||
scale_y_mic(),
|
||||
"gg"
|
||||
)
|
||||
expect_inherits(
|
||||
ggplot(
|
||||
data.frame(
|
||||
mic = as.mic(c(2, 4, 8, 16)),
|
||||
sir = as.sir(c("S", "I", "R", "SDD"))
|
||||
),
|
||||
aes(x = sir, y = mic)
|
||||
) +
|
||||
geom_col() +
|
||||
scale_y_mic(mic_range = c(4, 16)) +
|
||||
scale_x_sir(),
|
||||
"gg"
|
||||
)
|
||||
}
|
||||
|
||||
@ -109,7 +109,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
example_isolates$AMX %>% proportion_R()
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
# expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, sir_confidence_interval)))
|
||||
}
|
||||
|
||||
|
||||
@ -88,18 +88,18 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
expect_equal(sum(is.sir(example_isolates)), 40)
|
||||
|
||||
expect_stdout(print(tibble(ab = as.sir("S"))))
|
||||
|
||||
expect_true(example_isolates %>%
|
||||
select(AMC, MEM) %>%
|
||||
mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>%
|
||||
pull(MEM) %>%
|
||||
is.sir())
|
||||
|
||||
expect_true(example_isolates %>%
|
||||
select(AMC, MEM) %>%
|
||||
mutate(MEM = if_else(AMC == "S", "S", MEM)) %>%
|
||||
pull(MEM) %>%
|
||||
is.sir())
|
||||
|
||||
expect_true(example_isolates %>%
|
||||
select(AMC, MEM) %>%
|
||||
mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>%
|
||||
pull(MEM) %>%
|
||||
is.sir())
|
||||
|
||||
expect_true(example_isolates %>%
|
||||
select(AMC, MEM) %>%
|
||||
mutate(MEM = if_else(AMC == "S", "S", MEM)) %>%
|
||||
pull(MEM) %>%
|
||||
is.sir())
|
||||
}
|
||||
if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
|
||||
expect_inherits(
|
||||
@ -124,58 +124,78 @@ expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir
|
||||
|
||||
# Human -------------------------------------------------------------------
|
||||
|
||||
mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
|
||||
expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = FALSE, include_PKPD = FALSE)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R"))
|
||||
expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = TRUE, include_PKPD = FALSE)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "R"))
|
||||
expect_identical(as.character(as.sir(mics, mo = "Escherichia coli", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = FALSE, include_PKPD = FALSE)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R"))
|
||||
mics <- as.mic(2^c(-4:6)) # 0.0625 to 64 in factors of 2
|
||||
expect_identical(
|
||||
as.character(as.sir(mics,
|
||||
mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = FALSE, include_PKPD = FALSE
|
||||
)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R")
|
||||
)
|
||||
expect_identical(
|
||||
as.character(as.sir(mics,
|
||||
mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = TRUE, include_PKPD = FALSE
|
||||
)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "R")
|
||||
)
|
||||
expect_identical(
|
||||
as.character(as.sir(mics,
|
||||
mo = "Escherichia coli", ab = "AMC", guideline = "EUCAST 2022",
|
||||
uti = FALSE, include_PKPD = FALSE
|
||||
)),
|
||||
c("S", "S", "S", "S", "S", "S", "S", "S", "R", "R", "R")
|
||||
)
|
||||
|
||||
# test SIR using dplyr's mutate_if(...) and mutate(across(...))
|
||||
out1 <- as.sir(as.mic(c(0.256, 0.5, 1, 2)), mo = "Escherichia coli", ab = "ertapenem", guideline = "EUCAST 2023")
|
||||
expect_identical(out1, as.sir(c("S", "S", "R", "R")))
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
out2 <- data.frame(mo = "Escherichia coli",
|
||||
ab = "ertapenem",
|
||||
some_mics = as.mic(c(0.256, 0.5, 1, 2))) %>%
|
||||
mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) %>%
|
||||
out2 <- data.frame(
|
||||
mo = "Escherichia coli",
|
||||
ab = "ertapenem",
|
||||
some_mics = as.mic(c(0.256, 0.5, 1, 2))
|
||||
) %>%
|
||||
mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) %>%
|
||||
pull(some_mics)
|
||||
out3 <- data.frame(mo = "Escherichia coli",
|
||||
ab = "ertapenem",
|
||||
some_mics = as.mic(c(0.256, 0.5, 1, 2))) %>%
|
||||
mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") %>%
|
||||
out3 <- data.frame(
|
||||
mo = "Escherichia coli",
|
||||
ab = "ertapenem",
|
||||
some_mics = as.mic(c(0.256, 0.5, 1, 2))
|
||||
) %>%
|
||||
mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") %>%
|
||||
pull(some_mics)
|
||||
|
||||
|
||||
expect_identical(out1, out2)
|
||||
expect_identical(out1, out3)
|
||||
}
|
||||
|
||||
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
|
||||
expect_equal(suppressMessages(
|
||||
as.character(
|
||||
as.sir(
|
||||
x = as.mic(c(0.125, 0.5, 1, 2, 4)),
|
||||
mo = "B_STRPT_PNMN",
|
||||
ab = "AMP",
|
||||
guideline = "EUCAST 2020"
|
||||
expect_equal(
|
||||
suppressMessages(
|
||||
as.character(
|
||||
as.sir(
|
||||
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(suppressMessages(
|
||||
as.character(
|
||||
as.sir(
|
||||
x = as.mic(c(1, 2, 4, 8, 16)),
|
||||
mo = "B_STRPT_PNMN",
|
||||
ab = "AMX",
|
||||
guideline = "CLSI 2019"
|
||||
expect_equal(
|
||||
suppressMessages(
|
||||
as.character(
|
||||
as.sir(
|
||||
x = as.mic(c(1, 2, 4, 8, 16)),
|
||||
mo = "B_STRPT_PNMN",
|
||||
ab = "AMX",
|
||||
guideline = "CLSI 2019"
|
||||
)
|
||||
)
|
||||
)),
|
||||
),
|
||||
c("S", "S", "I", "R", "R")
|
||||
)
|
||||
|
||||
@ -241,20 +261,28 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
as.sir(guideline = "CLSI") %>%
|
||||
pull(amox_disk) %>%
|
||||
is.sir())
|
||||
|
||||
|
||||
# used by group_by() on sir_calc_df(), check some internals to see if grouped calculation without tidyverse works
|
||||
groups <- example_isolates %>%
|
||||
group_by(mo) %>%
|
||||
attributes() %>%
|
||||
.$groups
|
||||
expect_equal(nrow(groups),
|
||||
90)
|
||||
expect_equal(class(groups$.rows),
|
||||
c("vctrs_list_of", "vctrs_vctr", "list"))
|
||||
expect_equal(groups$.rows[[1]],
|
||||
c(101, 524, 1368))
|
||||
expect_equal(example_isolates[c(101, 524, 1368), "mo", drop = TRUE],
|
||||
rep(groups$mo[1], 3))
|
||||
expect_equal(
|
||||
nrow(groups),
|
||||
90
|
||||
)
|
||||
expect_equal(
|
||||
class(groups$.rows),
|
||||
c("vctrs_list_of", "vctrs_vctr", "list")
|
||||
)
|
||||
expect_equal(
|
||||
groups$.rows[[1]],
|
||||
c(101, 524, 1368)
|
||||
)
|
||||
expect_equal(
|
||||
example_isolates[c(101, 524, 1368), "mo", drop = TRUE],
|
||||
rep(groups$mo[1], 3)
|
||||
)
|
||||
}
|
||||
# frequency tables
|
||||
if (AMR:::pkg_is_available("cleaner")) {
|
||||
@ -295,27 +323,35 @@ expect_message(as.sir(data.frame(
|
||||
)))
|
||||
|
||||
# SDD vs I in CLSI 2024
|
||||
expect_identical(as.sir(as.mic(2 ^ c(-2:4)), mo = "Enterococcus faecium", ab = "Dapto", guideline = "CLSI 2024"),
|
||||
as.sir(c("SDD", "SDD", "SDD", "SDD", "SDD", "R", "R")))
|
||||
expect_identical(as.sir(as.mic(2 ^ c(-2:2)), mo = "Enterococcus faecium", ab = "Cipro
|
||||
expect_identical(
|
||||
as.sir(as.mic(2^c(-2:4)), mo = "Enterococcus faecium", ab = "Dapto", guideline = "CLSI 2024"),
|
||||
as.sir(c("SDD", "SDD", "SDD", "SDD", "SDD", "R", "R"))
|
||||
)
|
||||
expect_identical(
|
||||
as.sir(as.mic(2^c(-2:2)), mo = "Enterococcus faecium", ab = "Cipro
|
||||
", guideline = "CLSI 2024"),
|
||||
as.sir(c("S", "S", "S", "I", "R")))
|
||||
as.sir(c("S", "S", "S", "I", "R"))
|
||||
)
|
||||
|
||||
|
||||
# Veterinary --------------------------------------------------------------
|
||||
|
||||
sir_history <- sir_interpretation_history(clean = TRUE)
|
||||
|
||||
mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
|
||||
vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
|
||||
PRA = mics,
|
||||
FLR = mics,
|
||||
mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
|
||||
mics <- as.mic(2^c(-4:6)) # 0.0625 to 64 in factors of 2
|
||||
vet <- data.frame(
|
||||
animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
|
||||
PRA = mics,
|
||||
FLR = mics,
|
||||
mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1])
|
||||
)
|
||||
|
||||
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
|
||||
# host column name instead of values
|
||||
expect_identical(out_vet,
|
||||
as.sir(vet, host = "animal", guideline = "CLSI 2023"))
|
||||
expect_identical(
|
||||
out_vet,
|
||||
as.sir(vet, host = "animal", guideline = "CLSI 2023")
|
||||
)
|
||||
|
||||
# check outcomes
|
||||
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
|
||||
@ -326,11 +362,15 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11))
|
||||
expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
|
||||
|
||||
sir_history <- sir_interpretation_history()
|
||||
expect_identical(sort(sir_history$host),
|
||||
c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
|
||||
"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
|
||||
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
|
||||
"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry","poultry","poultry","poultry"))
|
||||
expect_identical(
|
||||
sort(sir_history$host),
|
||||
c(
|
||||
"cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
|
||||
"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
|
||||
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
|
||||
"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry", "poultry", "poultry", "poultry"
|
||||
)
|
||||
)
|
||||
|
||||
# ECOFF -------------------------------------------------------------------
|
||||
|
||||
@ -340,4 +380,3 @@ expect_equal(
|
||||
)
|
||||
# old method
|
||||
expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
|
||||
|
||||
|
||||
@ -29,11 +29,13 @@
|
||||
|
||||
# extra tests for {vctrs} pkg support
|
||||
if (AMR:::pkg_is_available("tibble")) {
|
||||
test <- tibble::tibble(ab = as.ab("CIP"),
|
||||
mo = as.mo("Escherichia coli"),
|
||||
mic = as.mic(2),
|
||||
disk = as.disk(20),
|
||||
sir = as.sir("S"))
|
||||
test <- tibble::tibble(
|
||||
ab = as.ab("CIP"),
|
||||
mo = as.mo("Escherichia coli"),
|
||||
mic = as.mic(2),
|
||||
disk = as.disk(20),
|
||||
sir = as.sir("S")
|
||||
)
|
||||
check1 <- lapply(test, class)
|
||||
test[1, "ab"] <- "GEN"
|
||||
test[1, "mo"] <- "B_KLBSL_PNMN"
|
||||
@ -45,9 +47,11 @@ if (AMR:::pkg_is_available("tibble")) {
|
||||
test[1, "sir"] <- "R"
|
||||
check2 <- lapply(test, class)
|
||||
expect_identical(check1, check2)
|
||||
|
||||
test <- tibble::tibble(cipro = as.sir("S"),
|
||||
variable = "test")
|
||||
|
||||
test <- tibble::tibble(
|
||||
cipro = as.sir("S"),
|
||||
variable = "test"
|
||||
)
|
||||
expect_equal(nrow(test[quinolones() == "S", ]), 1)
|
||||
expect_equal(nrow(test[quinolones() == "R", ]), 0)
|
||||
}
|
||||
|
||||
@ -146,14 +146,16 @@ for (i in seq_len(length(import_functions))) {
|
||||
fn <- names(import_functions)[i]
|
||||
pkg <- unname(import_functions[i])
|
||||
expect_true(pkg %in% suggests,
|
||||
info = paste0("package `", pkg, "` is not in Suggests"))
|
||||
info = paste0("package `", pkg, "` is not in Suggests")
|
||||
)
|
||||
# function should exist in foreign pkg namespace
|
||||
if (AMR:::pkg_is_available(pkg,
|
||||
also_load = FALSE,
|
||||
min_version = if (pkg == "dplyr") "1.0.0" else NULL
|
||||
also_load = FALSE,
|
||||
min_version = if (pkg == "dplyr") "1.0.0" else NULL
|
||||
)) {
|
||||
expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
|
||||
info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`"))
|
||||
info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
|
||||
)
|
||||
} else if (pkg != "rstudioapi") {
|
||||
warning("Package '", pkg, "' not available")
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user