mirror of https://github.com/msberends/AMR.git
107 lines
3.9 KiB
R
107 lines
3.9 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.gitlab.io/AMR. #
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# ==================================================================== #
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context("rsi.R")
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test_that("rsi works", {
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expect_true(as.rsi("S") < as.rsi("I"))
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expect_true(as.rsi("I") < as.rsi("R"))
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expect_true(as.rsi("R") > as.rsi("S"))
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expect_true(is.rsi(as.rsi("S")))
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# print plots, should not raise errors
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barplot(as.rsi(c("S", "I", "R")))
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plot(as.rsi(c("S", "I", "R")))
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print(as.rsi(c("S", "I", "R")))
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expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
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expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi",
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"<NA>" = "0",
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"Sum S" = "1",
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"Sum IR" = "1",
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"-Sum R" = "1",
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"-Sum I" = "0"))
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expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
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rep(FALSE, length(example_isolates)))
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library(dplyr)
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# 40 rsi columns
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expect_equal(example_isolates %>%
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mutate_at(vars(PEN:RIF), as.character) %>%
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lapply(is.rsi.eligible) %>%
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as.logical() %>%
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sum(),
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40)
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})
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test_that("mic2rsi works", {
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expect_equal(as.character(
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as.rsi(x = as.mic(0.125),
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mo = "B_STRPT_PNE",
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ab = "AMX",
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guideline = "EUCAST")),
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"S")
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expect_equal(as.character(
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as.rsi(x = as.mic(4),
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mo = "B_STRPT_PNE",
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ab = "AMX",
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guideline = "EUCAST")),
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"R")
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expect_true(example_isolates %>%
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mutate(amox_mic = as.mic(2)) %>%
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select(mo, amox_mic) %>%
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as.rsi() %>%
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pull(amox_mic) %>%
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is.rsi())
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})
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test_that("disk2rsi works", {
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expect_equal(as.character(
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as.rsi(x = as.disk(22),
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mo = "B_STRPT_PNE",
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ab = "ERY",
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guideline = "CLSI")),
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"S")
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expect_equal(as.character(
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as.rsi(x = as.disk(18),
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mo = "B_STRPT_PNE",
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ab = "ERY",
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guideline = "CLSI")),
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"I")
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expect_equal(as.character(
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as.rsi(x = as.disk(10),
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mo = "B_STRPT_PNE",
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ab = "ERY",
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guideline = "CLSI")),
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"R")
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expect_true(example_isolates %>%
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mutate(amox_disk = as.disk(15)) %>%
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select(mo, amox_disk) %>%
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as.rsi(guideline = "CLSI") %>%
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pull(amox_disk) %>%
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is.rsi())
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})
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