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README.md
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README.md
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<img src="man/figures/logo.png" align="right" height="120px" />
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### Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.
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**It contains documentation about all of the included functions and also a comprehensive tutorial about how to conduct AMR analysis.**
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## Development source
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*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.*
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*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.*
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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.
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## Authors
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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>,
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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>,
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Erwin E.A. Hassing<sup>2</sup>,
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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>,
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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>,
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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>
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Matthijs S. Berends<sup>1,2</sup>,
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Christian F. Luz<sup>1</sup>,
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Alex W. Friedrich1</sup>,
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Bhanu N.M. Sinha<sup>1</sup>,
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Casper J. Albers<sup>3</sup>,
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Corinna Glasner<sup>1</sup>
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<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>
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<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
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<sup>a</sup> Thesis dissertant<br>
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<sup>b</sup> Thesis advisor
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<sup>3</sup> Heymans Institute for Psychological Research, University of Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl)<br>
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<a href="https://www.rug.nl"><img src="man/figures/logo_rug.png" height="60px"></a>
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<a href="https://www.umcg.nl"><img src="man/figures/logo_umcg.png" height="60px"></a>
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@@ -32,40 +32,7 @@ Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https
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<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
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## How to get this package
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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.
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### Install from CRAN
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[](https://CRAN.R-project.org/package=AMR) [](https://CRAN.R-project.org/package=AMR)
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(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))
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- <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> Install using [RStudio](http://www.rstudio.com) (recommended):
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- Click on `Tools` and then `Install Packages...`
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- Type in `AMR` and press <kbd>Install</kbd>
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- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly:
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- `install.packages("AMR")`
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### Install from Zenodo
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[](https://doi.org/10.5281/zenodo.1305355)
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This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355
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### Install from GitLab
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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:
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Development Test | Result | Reference
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--- | :---: | ---
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All functions checked on Linux | [](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR)
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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)
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Percentage of syntax lines checked | [](https://codecov.io/gl/msberends/AMR) [](https://codecov.io/gl/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gl/msberends/AMR)
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If so, try it with:
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```r
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install.packages("devtools")
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devtools::install_gitlab("msberends/AMR")
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```
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Please see [our website](https://msberends.gitlab.io/AMR/#get-this-package).
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## Copyright
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