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AMR/R/zzz.R

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R
Executable File

# ==================================================================== #
# 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/ #
# ==================================================================== #
# set up package environment, used by numerous AMR functions
pkg_env <- new.env(hash = FALSE)
pkg_env$mo_failed <- character(0)
# determine info icon for messages
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(),
error = function(e) FALSE)
if (utf8_supported && !is_latex) {
# \u2139 is a symbol officially named 'information source'
pkg_env$info_icon <- "\u2139"
} else {
pkg_env$info_icon <- "i"
}
.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")
s3_register("ggplot2::ggplot", "rsi")
s3_register("ggplot2::ggplot", "mic")
s3_register("ggplot2::ggplot", "disk")
s3_register("ggplot2::ggplot", "resistance_predict")
# 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)
}