mirror of https://github.com/msberends/AMR.git
53 lines
2.1 KiB
R
53 lines
2.1 KiB
R
context("count.R")
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test_that("counts work", {
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# 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$amox),
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count_IR(septic_patients$amox))
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expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
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count_SI(septic_patients$amox))
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library(dplyr)
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expect_equal(septic_patients %>% count_S(amcl), 1057)
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expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
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expect_equal(septic_patients %>% count_all(amcl, gent), 1517)
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expect_identical(septic_patients %>% count_all(amcl, gent),
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septic_patients %>% count_S(amcl, gent) +
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septic_patients %>% count_IR(amcl, gent))
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# count of cases
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(cipro = count_S(cipr),
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genta = count_S(gent),
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combination = count_S(cipr, gent)) %>%
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pull(combination),
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c(192, 446, 184, 474))
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expect_equal(septic_patients %>% select(amox, cipr) %>% count_df(translate_ab = "official") %>% nrow(),
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6)
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# warning for speed loss
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expect_warning(count_R(as.character(septic_patients$amcl)))
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expect_warning(count_I(as.character(septic_patients$amcl)))
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expect_warning(count_S(as.character(septic_patients$amcl,
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septic_patients$gent)))
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expect_warning(count_S(septic_patients$amcl,
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as.character(septic_patients$gent)))
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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_df(c("A", "B", "C")))
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expect_error(count_df(septic_patients[,"date"]))
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})
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