mirror of https://github.com/msberends/AMR.git
185 lines
6.7 KiB
R
185 lines
6.7 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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/ #
|
|
# ==================================================================== #
|
|
|
|
context("rsi.R")
|
|
|
|
test_that("rsi works", {
|
|
|
|
skip_on_cran()
|
|
|
|
expect_true(as.rsi("S") < as.rsi("I"))
|
|
expect_true(as.rsi("I") < as.rsi("R"))
|
|
expect_true(is.rsi(as.rsi("S")))
|
|
|
|
x <- example_isolates$AMX
|
|
expect_s3_class(x[1], "rsi")
|
|
expect_s3_class(x[[1]], "rsi")
|
|
expect_s3_class(c(x[1], x[9]), "rsi")
|
|
expect_s3_class(unique(x[1], x[9]), "rsi")
|
|
|
|
pdf(NULL) # prevent Rplots.pdf being created
|
|
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
|
|
expect_silent(plot(as.rsi(c("S", "I", "R"))))
|
|
if (require("ggplot2")) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
|
|
expect_output(print(as.rsi(c("S", "I", "R"))))
|
|
|
|
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
|
|
|
|
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
|
|
|
|
expect_equal(summary(as.rsi(c("S", "R"))),
|
|
structure(c("Class" = "rsi",
|
|
"%R" = "50.0% (n=1)",
|
|
"%SI" = "50.0% (n=1)",
|
|
"- %S" = "50.0% (n=1)",
|
|
"- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
|
|
|
|
expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
|
|
rep(FALSE, length(example_isolates)))
|
|
|
|
library(dplyr, warn.conflicts = FALSE)
|
|
# 40 rsi columns
|
|
expect_equal(example_isolates %>%
|
|
mutate_at(vars(PEN:RIF), as.character) %>%
|
|
lapply(is.rsi.eligible) %>%
|
|
as.logical() %>%
|
|
sum(),
|
|
40)
|
|
|
|
expect_output(print(tibble(ab = as.rsi("S"))))
|
|
|
|
expect_error(as.rsi.mic(as.mic(16)))
|
|
expect_error(as.rsi.disk(as.disk(16)))
|
|
|
|
expect_error(get_guideline("this one does not exist"))
|
|
|
|
expect_s3_class(example_isolates %>%
|
|
mutate(m = as.mic(2),
|
|
d = as.disk(20)) %>%
|
|
skimr::skim(),
|
|
"data.frame")
|
|
expect_s3_class(skimr::skim(example_isolates),
|
|
"data.frame")
|
|
|
|
})
|
|
|
|
test_that("mic2rsi works", {
|
|
|
|
skip_on_cran()
|
|
|
|
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
|
|
expect_equal(as.character(
|
|
as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "AMP",
|
|
guideline = "EUCAST 2020")),
|
|
c("S", "S", "I", "I", "R"))
|
|
# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
|
|
expect_equal(as.character(
|
|
as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "AMX",
|
|
guideline = "CLSI 2019")),
|
|
c("S", "S", "I", "R", "R"))
|
|
|
|
# cutoffs at MIC = 8
|
|
expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
|
|
as.rsi("S"))
|
|
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
|
|
as.rsi("R"))
|
|
|
|
expect_true(suppressWarnings(example_isolates %>%
|
|
mutate(amox_mic = as.mic(2)) %>%
|
|
select(mo, amox_mic) %>%
|
|
as.rsi() %>%
|
|
pull(amox_mic) %>%
|
|
is.rsi()))
|
|
})
|
|
|
|
test_that("disk2rsi works", {
|
|
|
|
skip_on_cran()
|
|
|
|
expect_equal(as.character(
|
|
as.rsi(x = as.disk(22),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "ERY",
|
|
guideline = "CLSI")),
|
|
"S")
|
|
expect_equal(as.character(
|
|
as.rsi(x = as.disk(18),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "ERY",
|
|
guideline = "CLSI")),
|
|
"I")
|
|
expect_equal(as.character(
|
|
as.rsi(x = as.disk(10),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "ERY",
|
|
guideline = "CLSI")),
|
|
"R")
|
|
|
|
expect_true(example_isolates %>%
|
|
mutate(amox_disk = as.disk(15)) %>%
|
|
select(mo, amox_disk) %>%
|
|
as.rsi(guideline = "CLSI") %>%
|
|
pull(amox_disk) %>%
|
|
is.rsi())
|
|
|
|
# frequency tables
|
|
if (require("cleaner")) {
|
|
expect_s3_class(cleaner::freq(example_isolates$AMX), "freq")
|
|
}
|
|
})
|
|
|
|
test_that("data.frame2rsi works", {
|
|
|
|
skip_on_cran()
|
|
|
|
df <- data.frame(microorganism = "Escherichia coli",
|
|
AMP = as.mic(8),
|
|
CIP = as.mic(0.256),
|
|
GEN = as.disk(18),
|
|
TOB = as.disk(16),
|
|
ERY = "R", # note about assigning <rsi> class
|
|
CLR = "V") # note about cleaning
|
|
expect_s3_class(suppressWarnings(as.rsi(df)), "data.frame")
|
|
|
|
expect_s3_class(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
|
|
amoxi = c("R", "S", "I", "invalid")))$amoxi), "rsi")
|
|
expect_warning(data.frame(mo = "E. coli",
|
|
NIT = c("<= 2", 32)) %>%
|
|
as.rsi())
|
|
expect_message(data.frame(mo = "E. coli",
|
|
NIT = c("<= 2", 32),
|
|
uti = TRUE) %>%
|
|
as.rsi())
|
|
expect_message(
|
|
data.frame(mo = "E. coli",
|
|
NIT = c("<= 2", 32),
|
|
specimen = c("urine", "blood")) %>%
|
|
as.rsi())
|
|
})
|