diff --git a/.gitlab-ci.R b/.gitlab-ci.R index baaece8f..ae44cf34 100644 --- a/.gitlab-ci.R +++ b/.gitlab-ci.R @@ -2,18 +2,21 @@ # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # -# AUTHORS # -# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # +# SOURCE # +# https://gitlab.com/msberends/AMR # # # # LICENCE # -# This package is free software; you can redistribute it and/or modify # -# it under the terms of the GNU General Public License version 2.0, # -# as published by the Free Software Foundation. # +# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # -# This R package is distributed in the hope that it will be useful, # -# but WITHOUT ANY WARRANTY; without even the implied warranty of # -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # -# GNU General Public License version 2.0 for more details. # +# 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. # +# # +# This R package was created for academic research and was publicly # +# released in the hope that it will be useful, but it comes WITHOUT # +# ANY WARRANTY OR LIABILITY. # +# Visit our website for more info: https://msberends.gitab.io/AMR. # # ==================================================================== # install_if_needed <- function(pkg, repos, quiet) { @@ -43,14 +46,4 @@ gl_update_pkg_all <- function(repos = "https://cran.rstudio.com", print(instld[, c("Package", "Version")]) return(invisible(TRUE)) - - # which ones are needed now? - # pkg_needed <- - - # if (length(pkg_needed) > 0) { - # # install them - # for (i %in% 1:length(pkg_needed)) { - # install_if_needed(pkg = pkg_needed[i], repos = repos, quiet = quiet) - # } - # } } diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a87487f8..08439903 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -19,23 +19,18 @@ # Visit our website for more info: https://msberends.gitab.io/AMR. # # ==================================================================== # -# from https://stackoverflow.com/questions/51866926 -# and https://github.com/jangorecki/r.gitlab.ci -# and https://docs.gitlab.com/ce/ci/yaml/README.html -# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/ - stages: - build - test - deploy -# stretch only contains R 3.3 +# debian stretch only contains R 3.3... image: debian:buster-slim before_script: - apt-get update -qq # install dependencies for packages - - apt-get -y install -qq locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base + - apt-get install -qq locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base # set R system language - echo "LC_ALL=en_US.UTF-8" >> /etc/environment - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen @@ -47,8 +42,11 @@ before_script: - echo 'R_LIBS_USER="installed_deps"' >> .Renviron - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron - echo 'LANGUAGE="en_US.utf8"' >> .Renviron + - echo 'LANG="en_US.utf8"' >> .Renviron + - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron #- Rscript -e '.libPaths()' # install missing and outdated packages + - Rscript -e 'Sys.setlocale("LC_ALL", "en_US.UTF-8"); sessionInfo()' - Rscript -e 'sessionInfo()' - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' diff --git a/NEWS.md b/NEWS.md index b21e0fc8..03ffac5d 100755 --- a/NEWS.md +++ b/NEWS.md @@ -338,7 +338,6 @@ * Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations * Function `freq` to create **frequency tables**, with additional info in a header * Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines. - * Suggest your own via [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E) * [Exceptional resistances defined by EUCAST](http://www.eucast.org/expert_rules_and_intrinsic_resistance) are also supported instead of countries alone * Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively * New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate` diff --git a/R/zzz.R b/R/zzz.R index 101fe8d2..585052ac 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -23,7 +23,7 @@ #' #' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors. #' @details -#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods. +#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. #' #' This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). #' @section Read more on our website!: diff --git a/README.md b/README.md index 5ecf9764..9a44b87d 100755 --- a/README.md +++ b/README.md @@ -2,11 +2,9 @@ *NOTE: the original source code is on GitLab (https://gitlab.com/msberends/AMR), so you can report a bug at https://gitlab.com/msberends/AMR/issues. There is a mirror repository on GitHub (https://github.com/msberends/AMR). As the mirror process is automated by GitLab, both repositories always contain the latest changes.* ----- - ## Development source -This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with antibiotic properties by using evidence-based methods. +This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. **Not a developer? Then our website https://msberends.gitlab.io/AMR is probably a better place to read about this package.** It contains documentation about all of the included functions and also a comprehensive tutorial about how to conduct AMR analysis. diff --git a/docs/index.html b/docs/index.html index f787cd81..77395554 100644 --- a/docs/index.html +++ b/docs/index.html @@ -175,8 +175,8 @@

(TLDR - to find out how to conduct AMR analysis, please continue reading here to get started.

-

AMR is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with antibiotic properties by using evidence-based methods.

-

We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). We released this under the GNU General Public Licence v2.0 (GPL-2) which makes it free for everybody to use and distribute, for personal and commercial use, but it may not be used for patent purposes. Read further about our GPL-2 licence here.

+

AMR is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.

+

We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read further about our GPL-2 licence here.

This package is ready-to-use for a professional environment by specialists in the following fields:

Medical Microbiology: