AMR/inst/tinytest/test-proportion.R

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# ==================================================================== #
# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE CODE: #
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# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
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# #
# 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. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
# AMX resistance in `example_isolates`
expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
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expect_equal(sir_confidence_interval(example_isolates$AMX)[1], 0.5688204, tolerance = 0.0001)
expect_equal(sir_confidence_interval(example_isolates$AMX)[2], 0.6218738, tolerance = 0.0001)
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expect_equal(
1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
proportion_S(example_isolates$AMX)
)
expect_equal(
proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),
proportion_IR(example_isolates$AMX)
)
expect_equal(
proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
proportion_SI(example_isolates$AMX)
)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_equal(example_isolates %>% proportion_SI(AMC),
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0.7626397,
tolerance = 0.0001
)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
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0.9408,
tolerance = 0.0001
)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
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0.9382647,
tolerance = 0.0001
)
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# percentages
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expect_equal(
example_isolates %>%
group_by(ward) %>%
summarise(
R = proportion_R(CIP, as_percent = TRUE),
I = proportion_I(CIP, as_percent = TRUE),
S = proportion_S(CIP, as_percent = TRUE),
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n = n_sir(CIP),
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total = n()
) %>%
pull(n) %>%
sum(),
1409
)
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# count of cases
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expect_equal(
example_isolates %>%
group_by(ward) %>%
summarise(
cipro_p = proportion_SI(CIP, as_percent = TRUE),
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cipro_n = n_sir(CIP),
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genta_p = proportion_SI(GEN, as_percent = TRUE),
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genta_n = n_sir(GEN),
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combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
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combination_n = n_sir(CIP, GEN)
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) %>%
pull(combination_n),
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c(1181, 577, 116)
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)
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# proportion_df
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
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c(
example_isolates$AMX %>% proportion_SI(),
example_isolates$AMX %>% proportion_R()
)
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)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
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c(
example_isolates$AMX %>% proportion_S(),
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example_isolates$AMX %>% proportion_I(),
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example_isolates$AMX %>% proportion_R()
)
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)
# expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, sir_confidence_interval)))
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}
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# expect_warning(proportion_R(as.character(example_isolates$AMC)))
# expect_warning(proportion_S(as.character(example_isolates$AMC)))
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# expect_warning(proportion_S(as.character(example_isolates$AMC, example_isolates$GEN)))
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# expect_warning(n_sir(as.character(example_isolates$AMC, example_isolates$GEN)))
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expect_equal(
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suppressWarnings(n_sir(as.character(
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example_isolates$AMC,
example_isolates$GEN
))),
1879
)
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# check for errors
expect_error(proportion_IR("test", minimum = "test"))
expect_error(proportion_IR("test", as_percent = "test"))
expect_error(proportion_I("test", minimum = "test"))
expect_error(proportion_I("test", as_percent = "test"))
expect_error(proportion_S("test", minimum = "test"))
expect_error(proportion_S("test", as_percent = "test"))
expect_error(proportion_S("test", also_single_tested = TRUE))
# check too low amount of isolates
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expect_identical(
suppressWarnings(proportion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA_real_
)
expect_identical(
suppressWarnings(proportion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA_real_
)
expect_identical(
suppressWarnings(proportion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA_real_
)
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# warning for speed loss
# expect_warning(proportion_R(as.character(example_isolates$GEN)))
# expect_warning(proportion_I(as.character(example_isolates$GEN)))
# expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
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expect_error(proportion_df(c("A", "B", "C")))
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expect_error(proportion_df(example_isolates[, "date", drop = TRUE]))