2018-12-16 22:45:12 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
|
|
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
|
|
|
# #
|
|
|
|
|
# AUTHORS #
|
|
|
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
|
|
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
|
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
|
|
|
# as published by the Free Software Foundation. #
|
|
|
|
|
# #
|
|
|
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
|
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
|
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
|
|
|
# GNU General Public License version 2.0 for more details. #
|
|
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2018-08-25 22:01:14 +02:00
|
|
|
context("rsi.R")
|
|
|
|
|
|
|
|
|
|
test_that("rsi works", {
|
|
|
|
|
expect_true(as.rsi("S") < as.rsi("I"))
|
|
|
|
|
expect_true(as.rsi("I") < as.rsi("R"))
|
|
|
|
|
expect_true(as.rsi("R") > as.rsi("S"))
|
|
|
|
|
expect_true(is.rsi(as.rsi("S")))
|
|
|
|
|
|
|
|
|
|
# print plots, should not raise errors
|
|
|
|
|
barplot(as.rsi(c("S", "I", "R")))
|
|
|
|
|
plot(as.rsi(c("S", "I", "R")))
|
|
|
|
|
print(as.rsi(c("S", "I", "R")))
|
|
|
|
|
|
|
|
|
|
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
|
|
|
|
|
|
2018-12-07 12:04:55 +01:00
|
|
|
expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi",
|
2018-08-25 22:01:14 +02:00
|
|
|
"<NA>" = "0",
|
|
|
|
|
"Sum S" = "1",
|
|
|
|
|
"Sum IR" = "1",
|
|
|
|
|
"-Sum R" = "1",
|
|
|
|
|
"-Sum I" = "0"))
|
2018-11-02 14:55:29 +01:00
|
|
|
|
|
|
|
|
expect_identical(as.logical(lapply(septic_patients, is.rsi.eligible)),
|
|
|
|
|
rep(FALSE, length(septic_patients)))
|
|
|
|
|
|
|
|
|
|
library(dplyr)
|
|
|
|
|
# 40 rsi columns
|
2018-11-02 15:04:48 +01:00
|
|
|
expect_equal(septic_patients %>%
|
|
|
|
|
mutate_at(vars(peni:rifa), as.character) %>%
|
|
|
|
|
lapply(is.rsi.eligible) %>%
|
|
|
|
|
as.logical() %>%
|
|
|
|
|
sum(),
|
|
|
|
|
40)
|
2018-11-02 14:55:29 +01:00
|
|
|
|
2018-08-25 22:01:14 +02:00
|
|
|
})
|
