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153 lines
7.2 KiB
R
Executable File
153 lines
7.2 KiB
R
Executable File
# ==================================================================== #
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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.gitlab.io/AMR. #
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# ==================================================================== #
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context("portion.R")
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test_that("portions works", {
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# amox resistance in `septic_patients`
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expect_equal(portion_R(septic_patients$amox), 0.5557364, tolerance = 0.0001)
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expect_equal(portion_I(septic_patients$amox), 0.002441009, tolerance = 0.0001)
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expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
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portion_S(septic_patients$amox))
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expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
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portion_IR(septic_patients$amox))
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expect_equal(portion_S(septic_patients$amox) + portion_I(septic_patients$amox),
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portion_SI(septic_patients$amox))
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expect_equal(septic_patients %>% portion_S(amcl),
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0.7142097,
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tolerance = 0.0001)
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expect_equal(septic_patients %>% portion_S(amcl, gent),
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0.9232481,
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tolerance = 0.0001)
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expect_equal(septic_patients %>% portion_S(amcl, gent, also_single_tested = TRUE),
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0.926045,
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tolerance = 0.0001)
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# amcl+genta susceptibility around 92.3%
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expect_equal(suppressWarnings(rsi(septic_patients$amcl,
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septic_patients$gent,
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interpretation = "S")),
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0.9232481,
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tolerance = 0.000001)
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# percentages
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(R = portion_R(cipr, as_percent = TRUE),
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I = portion_I(cipr, as_percent = TRUE),
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S = portion_S(cipr, as_percent = TRUE),
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n = n_rsi(cipr),
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total = n()) %>%
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pull(n) %>%
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sum(),
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1409)
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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_p = portion_S(cipr, as_percent = TRUE),
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cipro_n = n_rsi(cipr),
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genta_p = portion_S(gent, as_percent = TRUE),
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genta_n = n_rsi(gent),
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combination_p = portion_S(cipr, gent, as_percent = TRUE),
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combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
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c(202, 488, 201, 499))
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expect_warning(portion_R(as.character(septic_patients$amcl)))
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expect_warning(portion_S(as.character(septic_patients$amcl)))
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expect_warning(portion_S(as.character(septic_patients$amcl,
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septic_patients$gent)))
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expect_warning(n_rsi(as.character(septic_patients$amcl,
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septic_patients$gent)))
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expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
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septic_patients$gent))),
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1879)
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# check for errors
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expect_error(portion_IR("test", minimum = "test"))
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expect_error(portion_IR("test", as_percent = "test"))
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expect_error(portion_I("test", minimum = "test"))
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expect_error(portion_I("test", as_percent = "test"))
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expect_error(portion_S("test", minimum = "test"))
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expect_error(portion_S("test", as_percent = "test"))
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expect_error(portion_S("test", also_single_tested = "test"))
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# check too low amount of isolates
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expect_identical(suppressWarnings(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
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NA)
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expect_identical(suppressWarnings(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
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NA)
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expect_identical(suppressWarnings(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
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NA)
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# warning for speed loss
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expect_warning(portion_R(as.character(septic_patients$gent)))
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expect_warning(portion_I(as.character(septic_patients$gent)))
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expect_warning(portion_S(septic_patients$amcl, as.character(septic_patients$gent)))
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})
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test_that("old rsi works", {
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# amox resistance in `septic_patients` should be around 58.53%
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expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5581774, tolerance = 0.0001)
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expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5581774, tolerance = 0.0001)
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# pita+genta susceptibility around 95.3%
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
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septic_patients$gent,
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interpretation = "S",
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info = TRUE)),
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0.9526814,
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tolerance = 0.0001)
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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_S = suppressWarnings(rsi(cipr, interpretation = "S",
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as_percent = TRUE, warning = FALSE)),
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cipro_n = n_rsi(cipr),
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genta_S = suppressWarnings(rsi(gent, interpretation = "S",
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as_percent = TRUE, warning = FALSE)),
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genta_n = n_rsi(gent),
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combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
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as_percent = TRUE, warning = FALSE)),
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combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
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c(202, 488, 201, 499))
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# portion_df
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expect_equal(
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septic_patients %>% select(amox) %>% portion_df() %>% pull(Value),
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c(septic_patients$amox %>% portion_S(),
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septic_patients$amox %>% portion_I(),
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septic_patients$amox %>% portion_R())
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)
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expect_equal(
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septic_patients %>% select(amox) %>% portion_df(combine_IR = TRUE) %>% pull(Value),
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c(septic_patients$amox %>% portion_S(),
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septic_patients$amox %>% portion_IR())
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)
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})
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