language

.gitlab-ci.R

@@ -2,18 +2,21 @@
 # TITLE                                                                #
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
-# AUTHORS                                                              #
+# SOURCE                                                               #
-# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
+# https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# This package is free software; you can redistribute it and/or modify #
+# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
-# it under the terms of the GNU General Public License version 2.0,    #
-# as published by the Free Software Foundation.                        #
 #                                                                      #
-# This R package is distributed in the hope that it will be useful,    #
+# This R package is free software; you can freely use and distribute   #
-# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
+# it for both personal and commercial purposes under the terms of the  #
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# GNU General Public License version 2.0 for more details.             #
+# 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)
-  #  }
-  # }
 }

.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)'
 

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`

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!:

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.
 

docs/index.html

@@ -175,8 +175,8 @@
 </h1></div>
 <p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
 <hr>
-<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of <strong>Antimicrobial Resistance (AMR)</strong> and to work with antibiotic properties by using evidence-based methods.</p>
+<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.</p>
-<p>We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; 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 <strong>not</strong> be used for patent purposes. Read further about our GPL-2 licence <a href="./LICENSE-text.html">here</a>.</p>
+<p>We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; 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 <strong>not</strong> 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 <a href="./LICENSE-text.html">here</a>.</p>
 <p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>
 <p>Medical Microbiology:</p>
 <ul>
@@ -214,7 +214,7 @@
 <div id="get-this-package" class="section level3">
 <h3 class="hasAnchor">
 <a href="#get-this-package" class="anchor"></a>Get this package</h3>
-<p>This package is available on the official R network. Install this package in R with:</p>
+<p>This package is available on the official R network (CRAN). Install this package in R with:</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</code></pre></div>
 <p>It will be downloaded and installed automatically.</p>
 </div>
@@ -257,7 +257,7 @@
 <li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li>
 </ol>
 <ul>
-<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used <a href="https://dplyr.tidyverse.org/#usage">with the <code>dplyr</code> package</a> (e.g. in conjunction with <a href="https://dplyr.tidyverse.org/reference/summarise.html"><code>summarise</code></a>)</li>
+<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
 <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
 <li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
 <li>Conduct descriptive statistics to enhance base R: calculate <code><a href="reference/kurtosis.html">kurtosis()</a></code>, <code><a href="reference/skewness.html">skewness()</a></code> and create frequency tables with <code><a href="reference/freq.html">freq()</a></code>

docs/news/index.html

@@ -597,8 +597,6 @@
 <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
 <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
 <li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.</li>
-<li>Suggest your own via <a href="https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&amp;body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E">https://github.com/msberends/AMR/issues/new</a>
-</li>
 <li>
 <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li>
 <li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>

docs/reference/AMR.html

@@ -223,7 +223,7 @@
         
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>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.</p>
+    <p>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.</p>
 <p>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 &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).</p>
     
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

index.md

@@ -4,9 +4,10 @@
 
 ----
 
-`AMR` is 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.
+`AMR` is 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.
 
-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](./LICENSE-text.html).
+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](./LICENSE-text.html).
 
 This package is ready-to-use for a professional environment by specialists in the following fields:
 
@@ -45,7 +46,8 @@ Developers:
 
 ### Get this package
 
-This package is available on the official R network. Install this package in R with:
+This package is available on the official R network (CRAN). Install this package in R with:
+
 ```r
 install.packages("AMR")
 ```
@@ -84,7 +86,7 @@ The `AMR` package basically does four important things:
 
 3. It **analyses the data** with convenient functions that use well-known methods.
 
-   * Calculate the resistance (and even co-resistance) of microbial isolates with the `portion_R()`, `portion_IR()`, `portion_I()`, `portion_SI()` and `portion_S()` functions. Similarly, the *number* of isolates can be determined with the `count_R()`, `count_IR()`, `count_I()`, `count_SI()` and `count_S()` functions. All these functions can be used [with the `dplyr` package](https://dplyr.tidyverse.org/#usage) (e.g. in conjunction with [`summarise`](https://dplyr.tidyverse.org/reference/summarise.html))
+   * Calculate the resistance (and even co-resistance) of microbial isolates with the `portion_R()`, `portion_IR()`, `portion_I()`, `portion_SI()` and `portion_S()` functions. Similarly, the *number* of isolates can be determined with the `count_R()`, `count_IR()`, `count_I()`, `count_SI()` and `count_S()` functions. All these functions can be used with the `dplyr` package (e.g. in conjunction with `summarise()`)
    * Plot AMR results with `geom_rsi()`, a function made for the `ggplot2` package
    * Predict antimicrobial resistance for the nextcoming years using logistic regression models with the `resistance_predict()` function
    * Conduct descriptive statistics to enhance base R: calculate `kurtosis()`, `skewness()` and create frequency tables with `freq()`

man/AMR.Rd

@@ -7,7 +7,7 @@
 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).
 }