* 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`:
### 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<ahref="https://orcid.org/0000-0001-7620-1800"><imgsrc="https://cran.rstudio.com/web/orcid.svg"height="16px"></a><sup>1,2,a</sup>,
Christian F. Luz<ahref="https://orcid.org/0000-0001-5809-5995"><imgsrc="https://cran.rstudio.com/web/orcid.svg"height="16px"></a><sup>1,a</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>b</sup> Thesis advisor
<sup>3</sup> Heymans Institute for Psychological Research, University of Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl)<br>
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.
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 | [](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR)
All functions checked on Windows | [](https://ci.appveyor.com/project/msberends/amr-svxon) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/amr-svxon)
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.7.1.9067</span>
<spanclass="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><ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author. <ahref='https://orcid.org/0000-0001-5809-5995'target='orcid.widget'><imgsrc='https://members.orcid.org/sites/default/files/vector_iD_icon.svg'class='orcid'alt='ORCID'height='16'></a>
<p><strong><ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <ahref='https://orcid.org/0000-0001-5809-5995'target='orcid.widget'><imgsrc='https://members.orcid.org/sites/default/files/vector_iD_icon.svg'class='orcid'alt='ORCID'height='16'></a>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.7.1.9067</span>
<spanclass="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 @@
<ahref="#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 <ahref="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: <ahref="https://cran-logs.rstudio.com">CRAN logs, 2019</a>)</small>.</p>
<p>After installing this package, R knows <ahref="./reference/microorganisms.html"><strong>~70,000 microorganisms</strong></a> (distinct microbial species) and <ahref="./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 & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <ahref="./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 <ahref="./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 & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <ahref="./news">actively maintained</a> and is free software (see <ahref="#copyright">Copyright</a>).</p>
<p><strong>Used to SPSS?</strong> Read our <ahref="./articles/SPSS.html">tutorial on how to import data from SPSS, SAS or Stata</a>.</p>
<p>This R package is free, open-source software and licensed under the <ahref="./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>
<ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a><br><smallclass="roles"> Author, maintainer </small><ahref="https://orcid.org/0000-0001-7620-1800"target="orcid.widget"><imgsrc="https://members.orcid.org/sites/default/files/vector_iD_icon.svg"class="orcid"alt="ORCID"height="16"></a></li>
<li>
<ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a><br><smallclass="roles"> Author </small><ahref="https://orcid.org/0000-0001-5809-5995"target="orcid.widget"><imgsrc="https://members.orcid.org/sites/default/files/vector_iD_icon.svg"class="orcid"alt="ORCID"height="16"></a></li>
<ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a><br><smallclass="roles"> Author, contributor</small><ahref="https://orcid.org/0000-0001-5809-5995"target="orcid.widget"><imgsrc="https://members.orcid.org/sites/default/files/vector_iD_icon.svg"class="orcid"alt="ORCID"height="16"></a></li>
<li>
<ahref="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a><br><smallclass="roles"> Author, thesis advisor </small><ahref="https://orcid.org/0000-0003-4881-038X"target="orcid.widget"><imgsrc="https://members.orcid.org/sites/default/files/vector_iD_icon.svg"class="orcid"alt="ORCID"height="16"></a></li>
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).
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).
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)).
**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.