AMR/tests/testthat/test-portion.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
context("portion.R")
test_that("portions works", {
# amox resistance in `septic_patients`
expect_equal(portion_R(septic_patients$amox), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
portion_S(septic_patients$amox))
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
portion_IR(septic_patients$amox))
expect_equal(portion_S(septic_patients$amox) + portion_I(septic_patients$amox),
portion_SI(septic_patients$amox))
expect_equal(septic_patients %>% portion_S(amcl),
0.7142097,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.9232481,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_S(amcl, gent, also_single_tested = TRUE),
0.926045,
tolerance = 0.0001)
# amcl+genta susceptibility around 92.3%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
septic_patients$gent,
interpretation = "S")),
0.9232481,
tolerance = 0.000001)
# percentages
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(R = portion_R(cipr, as_percent = TRUE),
I = portion_I(cipr, as_percent = TRUE),
S = portion_S(cipr, as_percent = TRUE),
n = n_rsi(cipr),
total = n()) %>%
pull(n) %>%
sum(),
1409)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
cipro_n = n_rsi(cipr),
genta_p = portion_S(gent, as_percent = TRUE),
genta_n = n_rsi(gent),
combination_p = portion_S(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 488, 201, 499))
expect_warning(portion_R(as.character(septic_patients$amcl)))
expect_warning(portion_S(as.character(septic_patients$amcl)))
expect_warning(portion_S(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_warning(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent))),
1879)
# check for errors
expect_error(portion_IR("test", minimum = "test"))
expect_error(portion_IR("test", as_percent = "test"))
expect_error(portion_I("test", minimum = "test"))
expect_error(portion_I("test", as_percent = "test"))
expect_error(portion_S("test", minimum = "test"))
expect_error(portion_S("test", as_percent = "test"))
expect_error(portion_S("test", also_single_tested = "test"))
# check too low amount of isolates
expect_identical(suppressWarnings(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
expect_identical(suppressWarnings(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
expect_identical(suppressWarnings(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
# warning for speed loss
expect_warning(portion_R(as.character(septic_patients$gent)))
expect_warning(portion_I(as.character(septic_patients$gent)))
expect_warning(portion_S(septic_patients$amcl, as.character(septic_patients$gent)))
})
test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 58.53%
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5581774, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5581774, tolerance = 0.0001)
# pita+genta susceptibility around 95.3%
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9526814,
tolerance = 0.0001)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
cipro_n = n_rsi(cipr),
genta_S = suppressWarnings(rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
genta_n = n_rsi(gent),
combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 488, 201, 499))
# portion_df
expect_equal(
septic_patients %>% select(amox) %>% portion_df() %>% pull(Value),
c(septic_patients$amox %>% portion_S(),
septic_patients$amox %>% portion_I(),
septic_patients$amox %>% portion_R())
)
expect_equal(
septic_patients %>% select(amox) %>% portion_df(combine_IR = TRUE) %>% pull(Value),
c(septic_patients$amox %>% portion_S(),
septic_patients$amox %>% portion_IR())
)
})