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https://github.com/msberends/AMR.git
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(v0.7.1.9102) lintr
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@ -37,13 +37,13 @@ test_that("ab_property works", {
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expect_identical(ab_name("Fluclox"), "Flucloxacillin")
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expect_identical(ab_name("fluklox"), "Flucloxacillin")
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expect_identical(ab_name("floxapen"), "Flucloxacillin")
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expect_identical(ab_name(21319) , "Flucloxacillin")
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expect_identical(ab_name(21319), "Flucloxacillin")
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expect_identical(ab_name("J01CF05"), "Flucloxacillin")
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expect_identical(ab_ddd("AMX", "oral"), 1)
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expect_identical(ab_ddd("AMX", "oral", units = TRUE) , "g")
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expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g")
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expect_identical(ab_ddd("AMX", "iv"), 1)
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expect_identical(ab_ddd("AMX", "iv", units = TRUE) , "g")
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expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g")
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expect_identical(ab_name(x = c("AMC", "PLB")), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
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expect_identical(ab_name(x = c("AMC", "PLB"), tolower = TRUE),
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@ -85,6 +85,6 @@ test_that("counts work", {
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expect_error(count_S("test", as_percent = "test"))
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expect_error(count_df(c("A", "B", "C")))
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expect_error(count_df(example_isolates[,"date"]))
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expect_error(count_df(example_isolates[, "date"]))
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})
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@ -41,9 +41,8 @@ test_that("data sets are valid", {
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# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
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datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
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for (i in 1:length(datasets)) {
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for (i in seq_len(length(datasets))) {
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dataset <- get(datasets[i], envir = asNamespace("AMR"))
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#print(paste("testing data set", datasets[i]))
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expect_identical(dataset_UTF8_to_ASCII(dataset), dataset)
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}
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})
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@ -33,16 +33,12 @@ test_that("first isolates work", {
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na.rm = TRUE),
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1317)
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# first *weighted* isolates
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# first weighted isolates
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
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# let syntax determine these automatically:
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# col_date = "date",
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# col_patient_id = "patient_id",
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# col_mo = "mo",
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# col_keyantibiotics = "keyab",
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# let syntax determine arguments automatically
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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@ -145,7 +141,7 @@ test_that("first isolates work", {
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filter_specimen = "something_unexisting")))
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# printing of exclusion message
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expect_output(example_isolates %>%
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expect_message(example_isolates %>%
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first_isolate(col_date = "date",
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col_mo = "mo",
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col_patient_id = "patient_id",
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@ -34,4 +34,3 @@ test_that("frequency table works", {
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library(dplyr)
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expect_true(is.freq(example_isolates %>% freq(AMX)))
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})
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@ -60,7 +60,7 @@ test_that("G-test works", {
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y = c(780, 1560, 780),
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rescale.p = TRUE))
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expect_error(g.test(matrix(data = c(-1, -2, -3 , -4), ncol = 2, byrow = TRUE)))
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expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
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expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
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})
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@ -30,7 +30,6 @@ test_that("get_locale works", {
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expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
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expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
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expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
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# expect_identical(mo_fullname("CoNS", "fr"), "Staphylococcus \u00e0 coagulase n\u00e9gative (CoNS)")
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expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")
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})
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@ -30,35 +30,26 @@ test_that("ggplot_rsi works", {
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# data should be equal
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>%
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summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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)
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print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
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print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>%
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summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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)
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
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summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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)
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic",
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facet = "interpretation"))$data %>%
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summarise_all(count_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>%
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summarise_all(count_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(count_IR) %>% as.double()
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)
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# support for scale_type ab and mo
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@ -32,11 +32,11 @@ test_that("mdro works", {
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outcome <- mdro(example_isolates)
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outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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expect_equal(outcome %>% class(), c("ordered", "factor"))
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outcome <- mdro(example_isolates, "nl", info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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expect_equal(outcome %>% class(), c("ordered", "factor"))
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# example_isolates should have these finding using Dutch guidelines
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expect_equal(outcome %>% freq() %>% pull(count),
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@ -94,7 +94,7 @@ test_that("as.mo works", {
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rep("B_STPHY_AURS", 9))
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expect_identical(
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as.character(
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as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
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as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
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rep("B_ESCHR_COLI", 6))
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# unprevalent MO
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expect_identical(
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@ -114,13 +114,13 @@ test_that("as.mo works", {
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c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
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# check for Becker classification
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
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expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
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@ -150,7 +150,7 @@ test_that("as.mo works", {
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# select with one column
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expect_identical(
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.mo() %>%
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@ -160,9 +160,9 @@ test_that("as.mo works", {
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# select with two columns
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expect_identical(
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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pull(mo),
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.mo())
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@ -260,10 +260,6 @@ test_that("as.mo works", {
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expect_null(mo_failures())
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expect_true(example_isolates %>% pull(mo) %>% is.mo())
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# expect_equal(get_mo_code("test", "mo"), "test")
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# expect_equal(length(get_mo_code("Escherichia", "genus")),
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# nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
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expect_error(translate_allow_uncertain(5))
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# very old MO codes (<= v0.5.0)
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@ -57,7 +57,7 @@ test_that("mo_property works", {
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expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
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expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
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#expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
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expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
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# test integrity
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MOs <- AMR::microorganisms
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@ -117,5 +117,5 @@ test_that("portions works", {
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)
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expect_error(portion_df(c("A", "B", "C")))
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expect_error(portion_df(example_isolates[,"date"]))
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expect_error(portion_df(example_isolates[, "date"]))
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})
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