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(v0.8.0.9027) adding susceptibility() and resistance()
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@ -22,67 +22,67 @@
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context("count.R")
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test_that("counts work", {
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expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
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expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
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expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
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# AMX resistance in `example_isolates`
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expect_equal(count_R(example_isolates$AMX), 683)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(count_S(example_isolates$AMX), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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count_IR(example_isolates$AMX))
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expect_equal(count_S(example_isolates$AMX) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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expect_equal(count_R(example_isolates$AMX), 683)
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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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library(dplyr)
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expect_equal(example_isolates %>% count_S(AMC), 1342)
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expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
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expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
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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_S(AMC, GEN, only_all_tested = TRUE) +
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example_isolates %>% count_IR(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_SI(CIP),
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genta = count_SI(GEN),
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combination = count_SI(CIP, GEN)) %>%
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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$AMX %>% count_SI(),
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example_isolates$AMX %>% count_R())
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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(example_isolates$AMX %>% count_S(),
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example_isolates$AMX %>% count_IR())
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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(example_isolates$AMX %>% count_S(),
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c(suppressWarnings(example_isolates$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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expect_warning(count_R(as.character(example_isolates$AMC)))
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expect_warning(count_I(as.character(example_isolates$AMC)))
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expect_warning(count_S(as.character(example_isolates$AMC,
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example_isolates$GEN)))
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expect_warning(count_S(example_isolates$AMC,
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as.character(example_isolates$GEN)))
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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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# check for errors
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expect_error(count_IR("test", minimum = "test"))
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expect_error(count_IR("test", as_percent = "test"))
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expect_error(count_I("test", minimum = "test"))
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expect_error(count_I("test", as_percent = "test"))
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expect_error(count_S("test", minimum = "test"))
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expect_error(count_S("test", as_percent = "test"))
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expect_error(count_resistant("test", minimum = "test"))
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expect_error(count_resistant("test", as_percent = "test"))
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expect_error(count_susceptible("test", minimum = "test"))
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expect_error(count_susceptible("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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