mirror of https://github.com/msberends/AMR.git
76 lines
3.7 KiB
R
Executable File
76 lines
3.7 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# set up package environment, used by numerous AMR functions
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pkg_env <- new.env(hash = FALSE)
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pkg_env$mo_failed <- character(0)
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# determine info icon for messages
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utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
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is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(),
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error = function(e) FALSE)
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if (utf8_supported && !is_latex) {
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# \u2139 is a symbol officially named 'information source'
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pkg_env$info_icon <- "\u2139"
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} else {
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pkg_env$info_icon <- "i"
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}
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.onLoad <- function(libname, pkgname) {
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# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
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# without the need to depend on other packages. This was suggested by the
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# developers of the vctrs package:
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# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
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s3_register("pillar::pillar_shaft", "ab")
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s3_register("pillar::pillar_shaft", "mo")
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s3_register("pillar::pillar_shaft", "rsi")
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s3_register("pillar::pillar_shaft", "mic")
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s3_register("pillar::pillar_shaft", "disk")
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s3_register("tibble::type_sum", "ab")
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s3_register("tibble::type_sum", "mo")
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s3_register("tibble::type_sum", "rsi")
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s3_register("tibble::type_sum", "mic")
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s3_register("tibble::type_sum", "disk")
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# Support for frequency tables from the cleaner package
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s3_register("cleaner::freq", "mo")
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s3_register("cleaner::freq", "rsi")
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# Support from skim() from the skimr package
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s3_register("skimr::get_skimmers", "mo")
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s3_register("skimr::get_skimmers", "rsi")
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s3_register("skimr::get_skimmers", "mic")
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s3_register("skimr::get_skimmers", "disk")
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s3_register("ggplot2::ggplot", "rsi")
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s3_register("ggplot2::ggplot", "mic")
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s3_register("ggplot2::ggplot", "disk")
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s3_register("ggplot2::ggplot", "resistance_predict")
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# if mo source exists, fire it up (see mo_source())
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try({
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if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
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invisible(get_mo_source())
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}
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}, silent = TRUE)
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}
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