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How to
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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Source Code
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< h1 > The < code > AMR< / code > Package< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://gitlab.com/msberends/AMR/blob/master/R/amr.R' > < code > R/amr.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > AMR.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Welcome to the < code > AMR< / code > package.< / p >
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< / div >
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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 the taxonomy of microorganisms, since the package contains all microbial (sub)species from the < a href = 'http://www.catalogueoflife.org' > Catalogue of Life< / a > < / p > < / li >
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< 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 > Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records< / p > < / li >
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< li > < p > Determining first isolates to be used for AMR analysis< / 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 therapies< / p > < / li >
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< 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 >
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< li > < p > Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)< / p > < / li >
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< li > < p > Plotting antimicrobial resistance< / p > < / li >
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< li > < p > Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code< / p > < / li >
< li > < p > Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code< / p > < / li >
< li > < p > Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI< / p > < / li >
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< li > < p > Principal component analysis for AMR< / p > < / li >
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< / ul >
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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 comprehensive 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 >
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< p > For suggestions, comments or questions, please contact us at:< / p >
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< p > Matthijs S. Berends < br / >
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m.s.berends [at] umcg [dot] nl < br / >
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University of Groningen
Department of Medical Microbiology
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University Medical Center Groningen < br / >
Post Office Box 30001 < br / >
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9700 RB Groningen < br / >
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The Netherlands< / p >
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< 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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< 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/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
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