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84 lines
3.8 KiB
R
84 lines
3.8 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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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$amox), 683)
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expect_equal(count_I(septic_patients$amox), 3)
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expect_equal(count_S(septic_patients$amox), 543)
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expect_equal(count_R(septic_patients$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$amox))
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library(dplyr)
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expect_equal(septic_patients %>% count_S(amcl), 1342)
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expect_equal(septic_patients %>% count_S(amcl, gent), 1660)
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expect_equal(septic_patients %>% count_all(amcl, gent), 1798)
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expect_identical(septic_patients %>% count_all(amcl, gent),
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septic_patients %>% count_S(amcl, gent) +
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septic_patients %>% count_IR(amcl, gent))
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# count of cases
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(cipro = count_S(cipr),
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genta = count_S(gent),
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combination = count_S(cipr, gent)) %>%
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pull(combination),
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c(192, 446, 184, 474))
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# count_df
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expect_equal(
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septic_patients %>% select(amox) %>% count_df() %>% pull(Value),
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c(septic_patients$amox %>% count_S(),
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septic_patients$amox %>% count_I(),
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septic_patients$amox %>% count_R())
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)
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expect_equal(
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septic_patients %>% select(amox) %>% count_df(combine_IR = TRUE) %>% pull(Value),
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c(septic_patients$amox %>% count_S(),
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septic_patients$amox %>% count_IR())
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)
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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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