mirror of https://github.com/msberends/AMR.git
137 lines
4.6 KiB
R
137 lines
4.6 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://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.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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skip_on_cran()
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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(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(as.character(as.rsi(c(1:3))), 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"))),
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structure(c("Class" = "rsi",
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"%R" = "50.0% (n=1)",
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"%SI" = "50.0% (n=1)",
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"- %S" = "50.0% (n=1)",
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"- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
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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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expect_output(print(tibble(ab = as.rsi("S"))))
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expect_error(as.rsi.mic(as.mic(16)))
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expect_error(as.rsi.disk(as.disk(16)))
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expect_error(get_guideline("this one does not exist"))
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})
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test_that("mic2rsi works", {
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skip_on_cran()
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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_PNMN",
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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_PNMN",
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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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expect_warning(data.frame(mo = "E. coli",
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NIT = c("<= 2", 32)) %>%
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as.rsi())
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expect_message(data.frame(mo = "E. coli",
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NIT = c("<= 2", 32),
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uti = TRUE) %>%
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as.rsi())
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expect_message(
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data.frame(mo = "E. coli",
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NIT = c("<= 2", 32),
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specimen = c("urine", "blood")) %>%
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as.rsi())
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})
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test_that("disk2rsi works", {
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skip_on_cran()
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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_PNMN",
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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_PNMN",
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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_PNMN",
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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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