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(v1.6.0.9023) new unit test flow
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@ -41,42 +41,6 @@ test_that("counts work", {
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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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library(dplyr, warn.conflicts = FALSE)
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expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
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expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
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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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# count of cases
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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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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# 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$AMX %>% count_resistant())
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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suppressWarnings(example_isolates$AMX %>% count_IR()))
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_R())
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)
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# warning for speed loss
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reset_all_thrown_messages()
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@ -94,11 +58,49 @@ test_that("counts work", {
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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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# grouping in rsi_calc_df() (= backbone of rsi_df())
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expect_true("hospital_id" %in% (example_isolates %>%
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group_by(hospital_id) %>%
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select(hospital_id, AMX, CIP, gender) %>%
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rsi_df() %>%
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colnames()))
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if (require("dplyr")) {
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expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
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expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
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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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# count of cases
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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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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# 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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)
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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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)
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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$AMX %>% count_S()),
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_R())
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)
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# grouping in rsi_calc_df() (= backbone of rsi_df())
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expect_true("hospital_id" %in% (example_isolates %>%
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group_by(hospital_id) %>%
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select(hospital_id, AMX, CIP, gender) %>%
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rsi_df() %>%
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colnames()))
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}
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})
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