mirror of
https://github.com/msberends/AMR.git
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(v0.8.0.9027) adding susceptibility() and resistance()
This commit is contained in:
@ -174,7 +174,6 @@ Function Bootstrap {
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Progress "Downloading and installing travis_tool.sh"
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cp "tests\appveyor\travis_tool.sh" "..\travis_tool.sh"
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# Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/master/tests/appveyor/travis_tool.sh -OutFile "..\travis_tool.sh"
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echo '@bash.exe ../travis_tool.sh %*' | Out-File -Encoding ASCII .\travis_tool.sh.cmd
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cat .\travis_tool.sh.cmd
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bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore"
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@ -22,67 +22,67 @@
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context("count.R")
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test_that("counts work", {
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expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
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expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
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expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
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# AMX resistance in `example_isolates`
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expect_equal(count_R(example_isolates$AMX), 683)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(count_S(example_isolates$AMX), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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count_IR(example_isolates$AMX))
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expect_equal(count_S(example_isolates$AMX) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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expect_equal(count_R(example_isolates$AMX), 683)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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suppressWarnings(count_IR(example_isolates$AMX)))
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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library(dplyr)
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expect_equal(example_isolates %>% count_S(AMC), 1342)
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expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
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expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
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expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
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expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
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expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
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expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
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expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
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expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
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example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE) +
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example_isolates %>% count_IR(AMC, GEN, only_all_tested = TRUE))
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example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
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example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
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# count of cases
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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summarise(cipro = count_SI(CIP),
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genta = count_SI(GEN),
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combination = count_SI(CIP, GEN)) %>%
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summarise(cipro = count_susceptible(CIP),
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genta = count_susceptible(GEN),
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combination = count_susceptible(CIP, GEN)) %>%
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pull(combination),
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c(253, 465, 192, 558))
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# count_df
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
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c(example_isolates$AMX %>% count_SI(),
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example_isolates$AMX %>% count_R())
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c(example_isolates$AMX %>% count_susceptible(),
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example_isolates$AMX %>% count_resistant())
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
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c(example_isolates$AMX %>% count_S(),
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example_isolates$AMX %>% count_IR())
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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suppressWarnings(example_isolates$AMX %>% count_IR()))
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
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c(example_isolates$AMX %>% count_S(),
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c(suppressWarnings(example_isolates$AMX %>% count_S()),
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_R())
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)
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# warning for speed loss
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expect_warning(count_R(as.character(example_isolates$AMC)))
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expect_warning(count_I(as.character(example_isolates$AMC)))
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expect_warning(count_S(as.character(example_isolates$AMC,
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example_isolates$GEN)))
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expect_warning(count_S(example_isolates$AMC,
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as.character(example_isolates$GEN)))
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expect_warning(count_resistant(as.character(example_isolates$AMC)))
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expect_warning(count_resistant(example_isolates$AMC,
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as.character(example_isolates$GEN)))
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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_resistant("test", minimum = "test"))
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expect_error(count_resistant("test", as_percent = "test"))
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expect_error(count_susceptible("test", minimum = "test"))
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expect_error(count_susceptible("test", as_percent = "test"))
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expect_error(count_df(c("A", "B", "C")))
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expect_error(count_df(example_isolates[, "date"]))
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@ -22,20 +22,12 @@
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context("deprecated.R")
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test_that("deprecated functions work", {
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# first 5 chars of official name
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expect_equal(suppressWarnings(as.character(as.atc(c("nitro", "cipro")))),
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c("J01XE01", "J01MA02"))
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# EARS-Net
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expect_equal(suppressWarnings(as.character(as.atc("AMX"))),
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"J01CA04")
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expect_equal(suppressWarnings(guess_ab_col(data.frame(AMP_ND10 = "R",
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AMC_ED20 = "S"),
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as.atc("augmentin"))),
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"AMC_ED20")
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expect_identical(suppressWarnings(p.symbol(seq(0, 1, 0.001))),
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p_symbol(seq(0, 1, 0.001)))
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expect_equal(suppressWarnings(portion_S(example_isolates$AMX)), proportion_S(example_isolates$AMX))
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expect_equal(suppressWarnings(portion_SI(example_isolates$AMX)), proportion_SI(example_isolates$AMX))
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expect_equal(suppressWarnings(portion_I(example_isolates$AMX)), proportion_I(example_isolates$AMX))
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expect_equal(suppressWarnings(portion_IR(example_isolates$AMX)), proportion_IR(example_isolates$AMX))
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expect_equal(suppressWarnings(portion_R(example_isolates$AMX)), proportion_R(example_isolates$AMX))
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})
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@ -30,26 +30,26 @@ test_that("ggplot_rsi works", {
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# data should be equal
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(resistance) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
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)
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print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
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print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(resistance) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
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)
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(portion_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(portion_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(resistance) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
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)
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expect_equal(
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_IR) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(count_IR) %>% as.double()
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(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_resistant) %>% as.double(),
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example_isolates %>% select(AMC, CIP) %>% summarise_all(count_resistant) %>% as.double()
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)
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# support for scale_type ab and mo
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@ -1,121 +0,0 @@
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# ==================================================================== #
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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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# AMX resistance in `example_isolates`
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expect_equal(portion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001)
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expect_equal(portion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001)
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expect_equal(1 - portion_R(example_isolates$AMX) - portion_I(example_isolates$AMX),
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portion_S(example_isolates$AMX))
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expect_equal(portion_R(example_isolates$AMX) + portion_I(example_isolates$AMX),
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portion_IR(example_isolates$AMX))
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expect_equal(portion_S(example_isolates$AMX) + portion_I(example_isolates$AMX),
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portion_SI(example_isolates$AMX))
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expect_equal(example_isolates %>% portion_SI(AMC),
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0.7626397,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% portion_SI(AMC, GEN),
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0.9408,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% portion_SI(AMC, GEN, only_all_tested = TRUE),
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0.9382647,
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tolerance = 0.0001)
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# percentages
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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summarise(R = portion_R(CIP, as_percent = TRUE),
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I = portion_I(CIP, as_percent = TRUE),
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S = portion_S(CIP, as_percent = TRUE),
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n = n_rsi(CIP),
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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(example_isolates %>%
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group_by(hospital_id) %>%
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summarise(cipro_p = portion_SI(CIP, as_percent = TRUE),
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cipro_n = n_rsi(CIP),
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genta_p = portion_SI(GEN, as_percent = TRUE),
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genta_n = n_rsi(GEN),
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combination_p = portion_SI(CIP, GEN, as_percent = TRUE),
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combination_n = n_rsi(CIP, GEN)) %>%
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pull(combination_n),
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c(305, 617, 241, 711))
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expect_warning(portion_R(as.character(example_isolates$AMC)))
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expect_warning(portion_S(as.character(example_isolates$AMC)))
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expect_warning(portion_S(as.character(example_isolates$AMC,
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example_isolates$GEN)))
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expect_warning(n_rsi(as.character(example_isolates$AMC,
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example_isolates$GEN)))
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expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
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example_isolates$GEN))),
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1879)
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# check for errors
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expect_error(portion_IR("test", minimum = "test"))
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expect_error(portion_IR("test", as_percent = "test"))
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expect_error(portion_I("test", minimum = "test"))
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expect_error(portion_I("test", as_percent = "test"))
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expect_error(portion_S("test", minimum = "test"))
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expect_error(portion_S("test", as_percent = "test"))
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expect_error(portion_S("test", also_single_tested = TRUE))
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# check too low amount of isolates
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expect_identical(suppressWarnings(portion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
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NA)
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expect_identical(suppressWarnings(portion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
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NA)
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expect_identical(suppressWarnings(portion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
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NA)
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# warning for speed loss
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expect_warning(portion_R(as.character(example_isolates$GEN)))
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expect_warning(portion_I(as.character(example_isolates$GEN)))
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expect_warning(portion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
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# portion_df
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expect_equal(
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example_isolates %>% select(AMX) %>% portion_df() %>% pull(value),
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c(example_isolates$AMX %>% portion_SI(),
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example_isolates$AMX %>% portion_R())
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
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c(example_isolates$AMX %>% portion_S(),
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example_isolates$AMX %>% portion_IR())
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)
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expect_equal(
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example_isolates %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
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c(example_isolates$AMX %>% portion_S(),
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example_isolates$AMX %>% portion_I(),
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example_isolates$AMX %>% portion_R())
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)
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expect_error(portion_df(c("A", "B", "C")))
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expect_error(portion_df(example_isolates[, "date"]))
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})
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124
tests/testthat/test-proportion.R
Executable file
124
tests/testthat/test-proportion.R
Executable file
@ -0,0 +1,124 @@
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# ==================================================================== #
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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 #
|
||||
# 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.gitlab.io/AMR. #
|
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# ==================================================================== #
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context("proportion.R")
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test_that("proportions works", {
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expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
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expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
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# AMX resistance in `example_isolates`
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expect_equal(proportion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001)
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expect_equal(proportion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001)
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expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
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proportion_S(example_isolates$AMX))
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expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),
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proportion_IR(example_isolates$AMX))
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expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
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proportion_SI(example_isolates$AMX))
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expect_equal(example_isolates %>% proportion_SI(AMC),
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0.7626397,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
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0.9408,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
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0.9382647,
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tolerance = 0.0001)
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# percentages
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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summarise(R = proportion_R(CIP, as_percent = TRUE),
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I = proportion_I(CIP, as_percent = TRUE),
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S = proportion_S(CIP, as_percent = TRUE),
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n = n_rsi(CIP),
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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(example_isolates %>%
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group_by(hospital_id) %>%
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summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE),
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cipro_n = n_rsi(CIP),
|
||||
genta_p = proportion_SI(GEN, as_percent = TRUE),
|
||||
genta_n = n_rsi(GEN),
|
||||
combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
|
||||
combination_n = n_rsi(CIP, GEN)) %>%
|
||||
pull(combination_n),
|
||||
c(305, 617, 241, 711))
|
||||
|
||||
expect_warning(proportion_R(as.character(example_isolates$AMC)))
|
||||
expect_warning(proportion_S(as.character(example_isolates$AMC)))
|
||||
expect_warning(proportion_S(as.character(example_isolates$AMC,
|
||||
example_isolates$GEN)))
|
||||
expect_warning(n_rsi(as.character(example_isolates$AMC,
|
||||
example_isolates$GEN)))
|
||||
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
|
||||
example_isolates$GEN))),
|
||||
1879)
|
||||
|
||||
# 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
|
||||
expect_identical(suppressWarnings(proportion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
|
||||
NA)
|
||||
expect_identical(suppressWarnings(proportion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
|
||||
NA)
|
||||
expect_identical(suppressWarnings(proportion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
|
||||
NA)
|
||||
|
||||
# warning for speed loss
|
||||
expect_warning(proportion_R(as.character(example_isolates$GEN)))
|
||||
expect_warning(proportion_I(as.character(example_isolates$GEN)))
|
||||
expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
|
||||
|
||||
# proportion_df
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
|
||||
c(example_isolates$AMX %>% proportion_SI(),
|
||||
example_isolates$AMX %>% proportion_R())
|
||||
)
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
|
||||
c(example_isolates$AMX %>% proportion_S(),
|
||||
example_isolates$AMX %>% proportion_IR())
|
||||
)
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
|
||||
c(example_isolates$AMX %>% proportion_S(),
|
||||
example_isolates$AMX %>% proportion_I(),
|
||||
example_isolates$AMX %>% proportion_R())
|
||||
)
|
||||
|
||||
expect_error(proportion_df(c("A", "B", "C")))
|
||||
expect_error(proportion_df(example_isolates[, "date"]))
|
||||
})
|
||||
Reference in New Issue
Block a user