mirror of https://github.com/msberends/AMR.git
34 lines
4.3 KiB
JSON
34 lines
4.3 KiB
JSON
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{
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"description": "<p>This R package contains functions to make <strong>microbiological, epidemiological data analysis easier</strong>. It allows the use of some new classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).</p>\n\n<p>With <code>AMR</code> you can also:</p>\n\n<ul>\n\t<li>Conduct AMR analysis with the <code>rsi</code> function, that can also be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise</code>) to calculate the resistance percentages (and even co-resistance) of different antibiotic columns of a table</li>\n\t<li>Predict antimicrobial resistance for the nextcoming years with the <code>rsi_predict</code> function</li>\n\t<li>Apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules to isolates</a> with the <code>EUCAST_rules</code> function</li>\n\t<li>Identify first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute) with the <code>first_isolate</code> function</li>\n\t<li>Get antimicrobial ATC properties from the WHO Collaborating Centre for Drug Statistics Methodology (<a href="https://www.whocc.no/atc_ddd_methodology/who_collaborating_centre/">WHOCC</a>), to be able to:\n\t<ul>\n\t\t<li>Translate antibiotic codes (like <em>AMOX</em>), official names (like <em>amoxicillin</em>) and even trade names (like <em>Amoxil</em> or <em>Trimox</em>) to an <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no">ATC code</a> (like <em>J01CA04</em>) and vice versa with the <code>abname</code> function</li>\n\t\t<li>Get the latest antibiotic properties like hierarchic groups and <a href="https://en.wikipedia.org/wiki/Defined_daily_dose">defined daily dose</a> (DDD) with units and administration form from the WHOCC website with the <code>atc_property</code> function</li>\n\t</ul>\n\t</li>\n\t<li>Create frequency tables with the <code>freq</code> function</li>\n</ul>\n\n<p>And it contains:</p>\n\n<ul>\n\t<li>A recent data set with ~2500 human pathogenic microorganisms, including family, genus, species, gram stain and aerobic/anaerobic</li>\n\t<li>A recent data set with all antibiotics as defined by the <a href="https://www.whocc.no/atc_ddd_methodology/who_collaborating_centre/">WHOCC</a>, including ATC code, official name and DDD's</li>\n\t<li>An example data set <code>septic_patients</code>, consisting of 2000 blood culture isolates from anonymised septic patients between 2001 and 2017.</li>\n</ul>\n\n<p>With the <code>MDRO</code> function (abbreviation of Multi Drug Resistant Organisms), you can check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: <a href="https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E">https://github.com/msberends/AMR/issues/new</a>.</p>\n",
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"license": "GPL-2.0",
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"title": "AMR: An R package to simplify the analysis and prediction of Antimicrobial Resistance and work with antibiotic properties by using evidence-based methods.",
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"version": "v0.2.0.9008",
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"upload_type": "software",
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"publication_date": "2018-07-04",
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"creators": [
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{
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"orcid": "0000-0001-7620-1800",
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"affiliation": "University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands",
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"name": "Matthijs S. Berends"
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},
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{
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"orcid": "0000-0001-5809-5995",
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"affiliation": "University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands",
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"name": "Christian F. Luz"
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}
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],
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"access_right": "open",
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"related_identifiers": [
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{
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"scheme": "url",
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"identifier": "https://github.com/msberends/AMR",
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"relation": "isSupplementTo"
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},
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{
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"scheme": "doi",
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"identifier": "10.5281/zenodo.1305355",
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"relation": "isVersionOf"
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}
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]
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}
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