P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:41:58 +02:00
Code Releases Activity

New mo algorithm, prepare for 2.0

Browse Source
This commit is contained in:
Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
committed by GitHub
parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
tests/tinytest.R
View File

@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -23,15 +27,45 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# we use {tinytest} instead of {testthat} because it does not rely on recent R versions - we want to test on R >= 3.0.
# Run them in RStudio using:
# rstudioapi::jobRunScript("tests/tinytest.R", name = "Tinytest Unit Tests", workingDir = getwd(), exportEnv = "tinytest_results")
# test only on GitHub Actions and at home - not on CRAN as tests are lengthy
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
library(AMR)
# set language
set_AMR_locale("English")
# set some functions if on old R
if (getRversion() < "3.2.0") {
anyNA <- AMR:::anyNA
dir.exists <- AMR:::dir.exists
file.size <- AMR:::file.size
file.mtime <- AMR:::file.mtime
isNamespaceLoaded <- AMR:::isNamespaceLoaded
lengths <- AMR:::lengths
}
if (getRversion() < "3.3.0") {
strrep <- AMR:::strrep
}
if (getRversion() < "3.5.0") {
isFALSE <- AMR:::isFALSE
}
if (getRversion() < "3.6.0") {
str2lang <- AMR:::str2lang
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
trimws <- AMR:::trimws
}
if (getRversion() < "4.0.0") {
deparse1 <- AMR:::deparse1
}
# start the unit tests
out <- test_package("AMR",
testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
testdir = ifelse(dir.exists("inst/tinytest"),
"inst/tinytest",
"tinytest"
),