mirror of https://github.com/msberends/AMR.git
78 lines
3.9 KiB
R
Executable File
78 lines
3.9 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) 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 analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
# set up package environment, used by numerous AMR functions
|
|
pkg_env <- new.env(hash = FALSE)
|
|
pkg_env$mo_failed <- character(0)
|
|
|
|
.onLoad <- function(libname, pkgname) {
|
|
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
|
|
# without the need to depend on other packages. This was suggested by the
|
|
# developers of the vctrs package:
|
|
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
|
|
s3_register("pillar::pillar_shaft", "ab")
|
|
s3_register("pillar::pillar_shaft", "mo")
|
|
s3_register("pillar::pillar_shaft", "rsi")
|
|
s3_register("pillar::pillar_shaft", "mic")
|
|
s3_register("pillar::pillar_shaft", "disk")
|
|
s3_register("tibble::type_sum", "ab")
|
|
s3_register("tibble::type_sum", "mo")
|
|
s3_register("tibble::type_sum", "rsi")
|
|
s3_register("tibble::type_sum", "mic")
|
|
s3_register("tibble::type_sum", "disk")
|
|
# Support for frequency tables from the cleaner package
|
|
s3_register("cleaner::freq", "mo")
|
|
s3_register("cleaner::freq", "rsi")
|
|
# Support from skim() from the skimr package
|
|
s3_register("skimr::get_skimmers", "mo")
|
|
s3_register("skimr::get_skimmers", "rsi")
|
|
s3_register("skimr::get_skimmers", "mic")
|
|
s3_register("skimr::get_skimmers", "disk")
|
|
|
|
# if mo source exists, fire it up (see mo_source())
|
|
try({
|
|
if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
|
|
invisible(get_mo_source())
|
|
}
|
|
}, silent = TRUE)
|
|
}
|
|
|
|
.onAttach <- function(...) {
|
|
# show notice in 10% of cases in interactive session
|
|
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
|
|
return()
|
|
}
|
|
packageStartupMessage(word_wrap("Thank you for using the AMR package! ",
|
|
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities: ",
|
|
font_blue("https://msberends.github.io/AMR/survey.html\n"),
|
|
"[prevent his notice with ",
|
|
font_bold("suppressPackageStartupMessages(library(AMR))"),
|
|
" or use ",
|
|
font_bold("options(AMR_silentstart = TRUE)"), "]"))
|
|
}
|
|
|
|
|
|
|