AMR/tests/testthat/test-count.R

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context("count.R")
test_that("counts work", {
# amox resistance in `septic_patients`
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expect_equal(count_R(septic_patients$amox), 662)
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expect_equal(count_I(septic_patients$amox), 3)
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expect_equal(count_S(septic_patients$amox), 335)
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expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
count_IR(septic_patients$amox))
expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
count_SI(septic_patients$amox))
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expect_equal(septic_patients %>% count_S(amcl), 1057)
expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
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# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro = count_S(cipr),
genta = count_S(gent),
combination = count_S(cipr, gent)) %>%
pull(combination),
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c(192, 446, 184, 474))
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expect_equal(septic_patients %>% select(amox, cipr) %>% count_df(translate_ab = "official") %>% nrow(),
6)
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# warning for speed loss
expect_warning(count_R(as.character(septic_patients$amcl)))
expect_warning(count_I(as.character(septic_patients$amcl)))
expect_warning(count_S(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_warning(count_S(septic_patients$amcl,
as.character(septic_patients$gent)))
# check for errors
expect_error(count_IR("test", minimum = "test"))
expect_error(count_IR("test", as_percent = "test"))
expect_error(count_I("test", minimum = "test"))
expect_error(count_I("test", as_percent = "test"))
expect_error(count_S("test", minimum = "test"))
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(septic_patients[,"date"]))
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})