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styled, unit test fix
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@ -9,7 +9,7 @@
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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@ -31,16 +31,22 @@ expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
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expect_equal(count_R(example_isolates$AMX), 804)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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suppressWarnings(count_IR(example_isolates$AMX)))
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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expect_equal(
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count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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suppressWarnings(count_IR(example_isolates$AMX))
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)
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expect_equal(
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suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX)
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)
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# warning for speed loss
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expect_warning(count_resistant(as.character(example_isolates$AMC)))
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expect_warning(count_resistant(example_isolates$AMC,
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as.character(example_isolates$GEN)))
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expect_warning(count_resistant(
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example_isolates$AMC,
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as.character(example_isolates$GEN)
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))
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# check for errors
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expect_error(count_resistant("test", minimum = "test"))
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@ -57,41 +63,53 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
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expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
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expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
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expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = 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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expect_identical(
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example_isolates %>% count_all(AMC, GEN, only_all_tested = 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(example_isolates %>%
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group_by(ward) %>%
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summarise(cipro = count_susceptible(CIP),
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genta = count_susceptible(GEN),
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combination = count_susceptible(CIP, GEN)) %>%
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pull(combination),
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c(253, 465, 192, 558))
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expect_equal(
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example_isolates %>%
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group_by(ward) %>%
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summarise(
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cipro = count_susceptible(CIP),
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genta = count_susceptible(GEN),
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combination = count_susceptible(CIP, GEN)
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) %>%
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pull(combination),
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c(253, 465, 192, 558)
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)
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# count_df
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
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c(example_isolates$AMX %>% count_susceptible(),
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example_isolates$AMX %>% count_resistant())
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c(
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example_isolates$AMX %>% count_susceptible(),
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example_isolates$AMX %>% count_resistant()
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)
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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suppressWarnings(example_isolates$AMX %>% count_IR()))
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c(
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suppressWarnings(example_isolates$AMX %>% count_S()),
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suppressWarnings(example_isolates$AMX %>% count_IR())
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)
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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c(
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suppressWarnings(example_isolates$AMX %>% count_S()),
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_R())
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example_isolates$AMX %>% count_R()
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)
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)
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# grouping in rsi_calc_df() (= backbone of rsi_df())
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expect_true("ward" %in% (example_isolates %>%
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group_by(ward) %>%
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select(ward, AMX, CIP, gender) %>%
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rsi_df() %>%
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colnames()))
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expect_true("ward" %in% (example_isolates %>%
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group_by(ward) %>%
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select(ward, AMX, CIP, gender) %>%
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rsi_df() %>%
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colnames()))
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}
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