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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</small>
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<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<p>Note: to keep the package size as small as possible, we only included
this vignette on CRAN. You can read more vignettes on our website about
how to conduct AMR data analysis, determine MDROs, find explanation of
EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<hr>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and
open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
dependencies</a> to simplify the analysis and prediction of
Antimicrobial Resistance (AMR) and to work with microbial and
antimicrobial data and properties, by using evidence-based methods.
<strong>Our aim is to provide a standard</strong> for clean and
reproducible AMR data analysis, that can therefore empower
epidemiological analyses to continuously enable surveillance and
treatment evaluation in any setting.</p>
<p>This work was published in the Journal of Statistical Software
(Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial
species and all ~570 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid R/SI and MIC values. The integral
breakpoint guidelines from CLSI and EUCAST are included from the last 10
years. It supports and can read any data format, including WHONET
data.</p>
<p>The <code>AMR</code> package is available in English, Chinese,
Danish, Dutch, French, German, Greek, Italian, Japanese, Polish,
Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian.
Antimicrobial drug (group) names and colloquial microorganism names are
provided in these languages.</p>
<p>This package is fully independent of any other R package and works on
Windows, macOS and Linux with all versions of R since R-3.0 (April
2013). <strong>It was designed to work in any setting, including those
with very limited resources</strong>. Since its first public release in
early 2018, this package has been downloaded from more than 175
countries.</p>
<p>This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
<li>Reference for the taxonomy of microorganisms, since the package
contains all microbial (sub)species from the List of Prokaryotic names
with Standing in Nomenclature (LPSN) and the Global Biodiversity
Information Facility (GBIF)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest
CLSI or EUCAST guidelines</li>
<li>Retrieving antimicrobial drug names, doses and forms of
administration from clinical health care records</li>
<li>Determining first isolates to be used for AMR data analysis</li>
<li>Calculating antimicrobial resistance</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
<li>Predicting future antimicrobial resistance using regression models</li>
<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
organisms (MDRO)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and
combination therapies</li>
<li>Predicting future antimicrobial resistance using regression
models</li>
<li>Getting properties for any microorganism (like Gram stain, species,
genus or family)</li>
<li>Getting properties for any antibiotic (like name, code of
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
<li>Plotting antimicrobial resistance</li>
<li>Applying EUCAST expert rules</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a
microorganism based on a SNOMED code</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an
antibiotic based on a LOINC code</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
translate MIC values and disk diffusion diameters to R/SI</li>
<li>Principal component analysis for AMR</li>
</ul>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and is being <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<p>All reference data sets (about microorganisms, antibiotics, R/SI
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
publicly and freely available. We continually export our data sets to
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
files that are machine-readable and suitable for input in any software
program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
download links on our website</a>, which is automatically updated with
every code change.</p>
<p>This R package was created for both routine data analysis and
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
is being <a href="./news">actively and durably maintained</a> by two
public healthcare organisations in the Netherlands.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. </small></p>
<p><small> This AMR package for R is free, open-source software and
licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General
Public License v2.0 (GPL-2)</a>. These requirements are consequently
legally binding: modifications must be released under the same license
when distributing the package, changes made to the code must be
documented, source code must be made available when the package is
distributed, and a copy of the license and copyright notice must be
included with the package. </small></p>
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