(v0.7.1.9068) gramstain to freq()

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: AMR
-Version: 0.7.1.9067
+Version: 0.7.1.9068
-Date: 2019-08-28
+Date: 2019-08-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
            family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")),
-    person(role = "aut",
+    person(role = c("aut", "ctb"),
            family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
     person(role = c("aut", "ths"),
            family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),

LICENSE

@@ -6,55 +6,23 @@ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.
 
-Preamble
+A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
 
-The licenses for most software are designed to take away your
+This R package, with package name 'AMR':
-freedom to share and change it.  By contrast, the GNU General Public
+- May be used for commercial purposes
-License is intended to guarantee your freedom to share and change free
+- May be used for private purposes
-software--to make sure the software is free for all its users.  This
+- May NOT be used for patent purposes
-General Public License applies to most of the Free Software
+- May be modified, although:
-Foundation's software and to any other program whose authors commit to
+  - Modifications MUST be released under the same license when distributing the package
-using it.  (Some other Free Software Foundation software is covered by
+  - Changes made to the code MUST be documented
-the GNU Lesser General Public License instead.)  You can apply it to
+- May be distributed, although:
-your programs, too.
+  - Source code MUST be made available when the package is distributed
+  - A copy of the license and copyright notice MUST be included with the package.
+- Comes with a LIMITATION of liability
+- Comes with NO warranty
 
-  When we speak of free software, we are referring to freedom, not
+END OF THE SUMMARY
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
 
-  To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have.  You must make sure that they, too, receive or can get the
-source code.  And you must show them these terms so they know their
-rights.
-
-  We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-
-  Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software.  If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
-authors' reputations.
-
-  Finally, any free program is threatened constantly by software
-patents.  We wish to avoid the danger that redistributors of a free
-program will individually obtain patent licenses, in effect making the
-program proprietary.  To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
-
-The precise terms and conditions for copying, distribution and
-modification follow.
 
 GNU GENERAL PUBLIC LICENSE
 TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9067
+# AMR 0.7.1.9068
 
 ### Breaking
 * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:

R/freq.R

@@ -29,11 +29,22 @@ clean::freq
 #' @export
 #' @noRd
 freq.mo <- function(x, ...) {
+  x_noNA <- x[!is.na(x)]
+  grams <- mo_gramstain(x_noNA, language = NULL)
   freq.default(x = x, ...,
-               .add_header = list(families = n_distinct(mo_family(x, language = NULL)),
+               .add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
-                                  genera = n_distinct(mo_genus(x, language = NULL)),
+                                                                  big.mark = ",",
-                                  species = n_distinct(paste(mo_genus(x, language = NULL),
+                                                                  decimal.mark = "."),
-                                                             mo_species(x, language = NULL)))))
+                                                           " (", percent(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), force_zero = TRUE),
+                                                           " of total)"),
+                                  `Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
+                                                                  big.mark = ",",
+                                                                  decimal.mark = "."),
+                                                           " (", percent(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), force_zero = TRUE),
+                                                           " of total)"),
+                                  genera = n_distinct(mo_genus(x_noNA, language = NULL)),
+                                  species = n_distinct(paste(mo_genus(x_noNA, language = NULL),
+                                                             mo_species(x_noNA, language = NULL)))))
 }
 
 #' @exportMethod freq.rsi

README.md

@@ -4,26 +4,26 @@
 <img src="man/figures/logo.png" align="right" height="120px" />
 
 ### Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) 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.**
 
 ## Development source
 
-*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.*
+*NOTE: the original source code is on GitLab (https://gitlab.com/msberends/AMR). 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.*
 
 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.
 
 ## Authors
-Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
+Matthijs S. Berends<sup>1,2</sup>,
-Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
+Christian F. Luz<sup>1</sup>,
-Erwin E.A. Hassing<sup>2</sup>,
+Alex W. Friedrich1</sup>,
-Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
+Bhanu N.M. Sinha<sup>1</sup>,
-Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
+Casper J. Albers<sup>3</sup>,
-Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
+Corinna Glasner<sup>1</sup>
   
 <sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
 <sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
-<sup>a</sup> Thesis dissertant<br>
+<sup>3</sup> Heymans Institute for Psychological Research, University of Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl)<br>
-<sup>b</sup> Thesis advisor
 
 <a href="https://www.rug.nl"><img src="man/figures/logo_rug.png" height="60px"></a>
 <a href="https://www.umcg.nl"><img src="man/figures/logo_umcg.png" height="60px"></a>
@@ -32,40 +32,7 @@ Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https
 <a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
 
 ## How to get this package
-All stable versions of this package [are published on CRAN](https://CRAN.R-project.org/package=AMR), the official R network with a peer-reviewed submission process.
+Please see [our website](https://msberends.gitlab.io/AMR/#get-this-package).
-
-### Install from CRAN
-[![CRAN_Badge](https://www.r-pkg.org/badges/version/AMR)](https://CRAN.R-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://CRAN.R-project.org/package=AMR)
-
-(Note: Downloads measured only by cran.rstudio.com, this excludes e.g. the official [cran.r-project.org](https://cran.r-project.org/package=AMR))
-
-- <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> Install using [RStudio](http://www.rstudio.com) (recommended):
-  - Click on `Tools` and then `Install Packages...`
-  - Type in `AMR` and press <kbd>Install</kbd>
-
-- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly:
-  - `install.packages("AMR")`
-
-### Install from Zenodo
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1305355.svg)](https://doi.org/10.5281/zenodo.1305355)
-
-This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355
-
-### Install from GitLab
-
-This is the latest **development version**. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green:
-
-Development Test | Result | Reference
---- | :---: | ---
-All functions checked on Linux | [![pipeline status](https://gitlab.com/msberends/AMR/badges/master/pipeline.svg)](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR) 
-All functions checked on Windows | [![AppVeyor_Build](https://ci.appveyor.com/api/projects/status/gitlab/msberends/AMR?branch=master&svg=true)](https://ci.appveyor.com/project/msberends/amr-svxon) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/amr-svxon)
-Percentage of syntax lines checked | [![Code_Coverage](https://codecov.io/gl/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gl/msberends/AMR) [![Code_Coverage](https://gitlab.com/msberends/AMR/badges/master/coverage.svg)](https://codecov.io/gl/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gl/msberends/AMR)
-
-If so, try it with:
-```r
-install.packages("devtools") 
-devtools::install_gitlab("msberends/AMR")
-```
 
 ## Copyright
 

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 
@@ -232,55 +232,23 @@ Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.
 
-Preamble
+A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
 
-The licenses for most software are designed to take away your
+This R package, with package name 'AMR':
-freedom to share and change it.  By contrast, the GNU General Public
+- May be used for commercial purposes
-License is intended to guarantee your freedom to share and change free
+- May be used for private purposes
-software--to make sure the software is free for all its users.  This
+- May NOT be used for patent purposes
-General Public License applies to most of the Free Software
+- May be modified, although:
-Foundation's software and to any other program whose authors commit to
+  - Modifications MUST be released under the same license when distributing the package
-using it.  (Some other Free Software Foundation software is covered by
+  - Changes made to the code MUST be documented
-the GNU Lesser General Public License instead.)  You can apply it to
+- May be distributed, although:
-your programs, too.
+  - Source code MUST be made available when the package is distributed
+  - A copy of the license and copyright notice MUST be included with the package.
+- Comes with a LIMITATION of liability
+- Comes with NO warranty
 
-  When we speak of free software, we are referring to freedom, not
+END OF THE SUMMARY
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
 
-  To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have.  You must make sure that they, too, receive or can get the
-source code.  And you must show them these terms so they know their
-rights.
-
-  We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-
-  Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software.  If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
-authors' reputations.
-
-  Finally, any free program is threatened constantly by software
-patents.  We wish to avoid the danger that redistributors of a free
-program will individually obtain patent licenses, in effect making the
-program proprietary.  To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
-
-The precise terms and conditions for copying, distribution and
-modification follow.
 
 GNU GENERAL PUBLIC LICENSE
 TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 
@@ -230,7 +230,7 @@
         </p>
       </li>
       <li>
-        <p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
+        <p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
         </p>
       </li>
       <li>

docs/extra.js

@@ -77,14 +77,17 @@ $( document ).ready(function() {
   // doctoral titles of authors
   function doct_tit(x) {
     if (typeof(x) != "undefined") {
-      x = x.replace("Alex", "Prof Dr Alex");
+      // authors
-      x = x.replace("Bhanu", "Prof Dr Bhanu");
+      x = x.replace(/Author, maintainer/g, "Main developer");
+      x = x.replace(/Author, contributor/g, "Main contributor");
+      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
+      x = x.replace("Alex", "Prof. Dr Alex");
+      x = x.replace("Bhanu", "Prof. Dr Bhanu");
+      x = x.replace("Casper", "Prof. Dr Casper");
       x = x.replace("Corinna", "Dr Corinna");
-      x = x.replace("Casper", "Prof Dr Casper");
+      // others
       x = x.replace("Bart", "Dr Bart");
       x = x.replace("Dennis", "Dr Dennis");
-      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
-      x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
     }
     return(x);
   }

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 
@@ -194,7 +194,7 @@
 <a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
 <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. Since its first public release in early 2018, this package has been downloaded over 20,000 times from more than 40 countries <small>(source: <a href="https://cran-logs.rstudio.com">CRAN logs, 2019</a>)</small>.</p>
 <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 microorganisms</strong></a> (distinct microbial species) and <a href="./reference/antibiotics.html"><strong>~450 antibiotics</strong></a> by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
-<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and 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 the full license <a href="./LICENSE-text.html">here</a>.</p>
+<p>We created this package for both routine analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
 <p><strong>Used to SPSS?</strong> Read our <a href="./articles/SPSS.html">tutorial on how to import data from SPSS, SAS or Stata</a>.</p>
 <div id="partners" class="section level4">
 <h4 class="hasAnchor">
@@ -356,6 +356,32 @@
 </ol>
 </div>
 </div>
+<div id="copyright" class="section level3">
+<h3 class="hasAnchor">
+<a href="#copyright" class="anchor"></a>Copyright</h3>
+<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
+<ul>
+<li><p>May be used for commercial purposes</p></li>
+<li><p>May be used for private purposes</p></li>
+<li><p>May <strong>not</strong> be used for patent purposes</p></li>
+<li>
+<p>May be modified, although:</p>
+<ul>
+<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
+<li>Changes made to the code <strong>must</strong> be documented</li>
+</ul>
+</li>
+<li>
+<p>May be distributed, although:</p>
+<ul>
+<li>Source code <strong>must</strong> be made available when the package is distributed</li>
+<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
+</ul>
+</li>
+<li><p>Comes with a LIMITATION of liability</p></li>
+<li><p>Comes with NO warranty</p></li>
+</ul>
+</div>
 </div>
   </div>
 
@@ -383,7 +409,7 @@
 <li>
 <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
 <li>
-<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
+<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
 <li>
 <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
 <li>

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9067" class="section level1">
+    <div id="amr-0-7-1-9068" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9067" class="anchor"></a>AMR 0.7.1.9067<small> Unreleased </small>
+<a href="#amr-0-7-1-9068" class="anchor"></a>AMR 0.7.1.9068<small> Unreleased </small>
 </h1>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
@@ -1258,7 +1258,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9067">0.7.1.9067</a></li>
+        <li><a href="#amr-0-7-1-9068">0.7.1.9068</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
       </span>
     </div>
 

index.md

@@ -10,8 +10,7 @@
 
 After installing this package, R knows [**~70,000 microorganisms**](./reference/microorganisms.html) (distinct microbial species) and [**~450 antibiotics**](./reference/antibiotics.html) by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data. 
 
-We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
+We created this package for both routine analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
-This R package is [actively maintained](./news) and 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 the full license [here](./LICENSE-text.html).
 
 **Used to SPSS?** Read our [tutorial on how to import data from SPSS, SAS or Stata](./articles/SPSS.html).
 
@@ -153,3 +152,27 @@ The `AMR` package basically does four important things:
        * Results of 40 antibiotics (each antibiotic in its own column) with a total ~40,000 antimicrobial results
        * Real and genuine data
      * The [`WHONET` data set](./reference/WHONET.html). This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET [on its tutorial page](./articles/WHONET.html).
+
+### Copyright
+
+This R package is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](./LICENSE-text.html). In a nutshell, this means that this package:
+
+- May be used for commercial purposes
+
+- May be used for private purposes
+
+- May **not** be used for patent purposes
+
+- May be modified, although:
+
+  - Modifications **must** be released under the same license when distributing the package
+  - Changes made to the code **must** be documented
+
+- May be distributed, although:
+
+  - Source code **must** be made available when the package is distributed
+  - A copy of the license and copyright notice **must** be included with the package.
+
+- Comes with a LIMITATION of liability
+
+- Comes with NO warranty

pkgdown/extra.js

@@ -77,14 +77,17 @@ $( document ).ready(function() {
   // doctoral titles of authors
   function doct_tit(x) {
     if (typeof(x) != "undefined") {
-      x = x.replace("Alex", "Prof Dr Alex");
+      // authors
-      x = x.replace("Bhanu", "Prof Dr Bhanu");
+      x = x.replace(/Author, maintainer/g, "Main developer");
+      x = x.replace(/Author, contributor/g, "Main contributor");
+      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
+      x = x.replace("Alex", "Prof. Dr Alex");
+      x = x.replace("Bhanu", "Prof. Dr Bhanu");
+      x = x.replace("Casper", "Prof. Dr Casper");
       x = x.replace("Corinna", "Dr Corinna");
-      x = x.replace("Casper", "Prof Dr Casper");
+      // others
       x = x.replace("Bart", "Dr Bart");
       x = x.replace("Dennis", "Dr Dennis");
-      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
-      x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
     }
     return(x);
   }

tests/testthat/test-freq.R

@@ -25,9 +25,13 @@ test_that("frequency table works", {
   library(clean)
   # mo
   expect_true(is.freq(freq(example_isolates$mo)))
+  # for this to work, the output of mo_gramstain() is to be expected as follows:
+  expect_equal(mo_gramstain("B_ESCHR_COL"), "Gram-negative")
+  expect_equal(mo_gramstain("B_STPHY_AUR"), "Gram-positive")
+  
   # rsi
   expect_true(is.freq(freq(example_isolates$AMX)))
   library(dplyr)
-  expect_true(is.freq(example_isolates %>% freq(mo)))
+  expect_true(is.freq(example_isolates %>% freq(AMX)))
 })