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Conduct AMR analysis
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Determine multi-drug resistance (MDR)
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Get properties of a microorganism
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Get properties of an antibiotic
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Create frequency tables
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< h1 > The < code > AMR< / code > Package< / h1 >
< div class = "hidden name" > < code > AMR.Rd< / code > < / div >
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< p > Welcome to the < code > AMR< / code > package.< / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > < code > AMR< / code > is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table 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 and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and 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.< / p >
< p > This package can be used for:< / p > < ul >
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< li > < p > Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life< / p > < / li >
< li > < p > Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines< / p > < / li >
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< li > < p > Calculating antimicrobial resistance< / p > < / li >
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< li > < p > Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)< / p > < / li >
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< li > < p > Calculating empirical susceptibility of both mono therapy and combination therapy< / p > < / li >
< li > < p > Predicting future antimicrobial resistance using regression models< / p > < / li >
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< li > < p > Getting properties for any microorganism (like Gram stain, species, genus or family)< / p > < / li >
< li > < p > Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)< / p > < / li >
< li > < p > Plotting antimicrobial resistance< / p > < / li >
< li > < p > Determining first isolates to be used for AMR analysis< / p > < / li >
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< li > < p > Applying EUCAST expert rules< / p > < / li >
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< li > < p > Descriptive statistics: frequency tables, kurtosis and skewness< / p > < / li >
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< h2 class = "hasAnchor" id = "authors" > < a class = "anchor" href = "#authors" > < / a > Authors< / h2 >
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< p > Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] < br / > < / p >
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< p > [1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - < a href = 'https://www.rug.nl' > https://www.rug.nl< / a > < a href = 'https://www.umcg.nl' > https://www.umcg.nl< / a > < br / >
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[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - < a href = 'certe.nl' > certe.nl< / a > < / p >
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< 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 >
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< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "contact-us" > < a class = "anchor" href = "#contact-us" > < / a > Contact us< / h2 >
< p > For suggestions, comments or questions, please contact us at:< / p >
< p > Matthijs S. Berends < br / >
m.s.berends [at] umcg [dot] nl < br / >
Department of Medical Microbiology, University of Groningen < br / >
University Medical Center Groningen < br / >
Post Office Box 30001 < br / >
9700 RB Groningen< / p >
< p > If you have found a bug, please file a new issue at: < br / >
< a href = 'https://gitlab.com/msberends/AMR/issues' > https://gitlab.com/msberends/AMR/issues< / a > < / p >
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< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
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