mirror of https://github.com/msberends/AMR.git
613 lines
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613 lines
26 KiB
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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Conduct AMR analysis
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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<a href="../articles/EUCAST.html">
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Apply EUCAST rules
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<a href="../reference/mo_property.html">
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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</a>
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<a href="../articles/freq.html">
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<span class="fa fa-sort-amount-down"></span>
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Create frequency tables
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</a>
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Use the G-test
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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Manual
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Changelog
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<a href="https://gitlab.com/msberends/AMR">
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Source Code
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Licence
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<div class="row">
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<div class="contents col-md-9">
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<div class="page-header">
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<h1>Reference</h1>
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</div>
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<table class="ref-index">
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<colgroup>
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<col class="alias" />
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<col class="title" />
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</colgroup>
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<tbody>
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<tr>
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<th colspan="2">
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<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
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<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
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</th>
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</tr>
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<tr>
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<td>
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<p><code><a href="AMR.html">AMR</a></code> </p>
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</td>
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<td><p>The <code>AMR</code> Package</p></td>
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</tr><tr>
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<td>
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<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
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</td>
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<td><p>The Catalogue of Life</p></td>
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</tr><tr>
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<td>
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<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
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</td>
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<td><p>Version info of included Catalogue of Life</p></td>
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</tr><tr>
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<td>
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<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
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</td>
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<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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<th colspan="2">
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<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
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<p class="section-desc"><p>Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a>.</p></p>
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</th>
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</tr>
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<tr>
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<td>
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<p><code><a href="as.ab.html">as.ab()</a></code> </p>
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</td>
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<td><p>Transform to antibiotic ID</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.atc.html">is.ab()</a></code> <code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p>
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</td>
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<td><p>Transform to ATC code</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
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</td>
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<td><p>Class 'disk'</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
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</td>
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<td><p>Class 'mic'</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
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</td>
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<td><p>Transform to microorganism ID</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
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</td>
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<td><p>Class 'rsi'</p></td>
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</tr><tr>
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<td>
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<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
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</td>
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<td><p>Use predefined reference data set</p></td>
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</tr><tr>
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<td>
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<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_rules_file()</a></code> </p>
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</td>
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<td><p>EUCAST rules</p></td>
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</tr><tr>
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<td>
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<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
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</td>
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<td><p>Data set for RSI interpretation</p></td>
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</tr><tr>
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<td>
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<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
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</td>
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<td><p>Guess antibiotic column</p></td>
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</tr><tr>
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<td>
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<p><code><a href="read.4D.html">read.4D()</a></code> </p>
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</td>
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<td><p>Read data from 4D database</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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<th colspan="2">
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<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
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<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
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</th>
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</tr>
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<tr>
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<td>
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<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
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</td>
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<td><p>Determine first (weighted) isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
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</td>
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<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
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</tr><tr>
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<td>
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<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
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</td>
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<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
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</td>
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<td><p>Property of a microorganism</p></td>
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</tr><tr>
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<td>
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<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
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</td>
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<td><p>Property of an antibiotic</p></td>
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</tr><tr>
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<td>
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<p><code><a href="age.html">age()</a></code> </p>
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</td>
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<td><p>Age in years of individuals</p></td>
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</tr><tr>
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<td>
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<p><code><a href="age_groups.html">age_groups()</a></code> </p>
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</td>
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<td><p>Split ages into age groups</p></td>
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</tr><tr>
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<td>
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<p><code><a href="p.symbol.html">p.symbol()</a></code> </p>
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</td>
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<td><p>Symbol of a p value</p></td>
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</tr><tr>
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<td>
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<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
|
||
</td>
|
||
<td><p>Join a table with <code>microorganisms</code></p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||
</td>
|
||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
|
||
<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="availability.html">availability()</a></code> </p>
|
||
</td>
|
||
<td><p>Check availability of columns</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
|
||
</td>
|
||
<td><p>Count isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p>
|
||
</td>
|
||
<td><p>Calculate resistance of isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
|
||
</td>
|
||
<td><p>Filter isolates on result in antibiotic class</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">freq()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i><frequency_tbl></i>)</a></code> </p>
|
||
</td>
|
||
<td><p>Frequency table</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="g.test.html">g.test()</a></code> </p>
|
||
</td>
|
||
<td><p><em>G</em>-test for Count Data</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p>
|
||
</td>
|
||
<td><p>AMR plots with <code>ggplot2</code></p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
|
||
</td>
|
||
<td><p>Kurtosis of the sample</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
|
||
</td>
|
||
<td><p>Predict antimicrobial resistance</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="skewness.html">skewness()</a></code> </p>
|
||
</td>
|
||
<td><p>Skewness of the sample</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2>
|
||
<p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="antibiotics.html">antibiotics</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with ~450 antibiotics</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with ~65,000 microorganisms</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="septic_patients.html">septic_patients</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with 2,000 blood culture isolates from septic patients</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
|
||
</td>
|
||
<td><p>Translation table for microorganism codes</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with previously accepted taxonomic names</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-other-functions" class="hasAnchor"><a href="#section-other-functions" class="anchor"></a>Other functions</h2>
|
||
<p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="translate.html">get_locale()</a></code> </p>
|
||
</td>
|
||
<td><p>Translate strings from AMR package</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> </p>
|
||
</td>
|
||
<td><p>Pattern Matching</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
|
||
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">abname()</a></code> <code><a href="AMR-deprecated.html">atc_property()</a></code> <code><a href="AMR-deprecated.html">atc_official()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">atc_name()</a></code> <code><a href="AMR-deprecated.html">atc_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">atc_tradenames()</a></code> </p>
|
||
</td>
|
||
<td><p>Deprecated functions</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||
<h2>Contents</h2>
|
||
<ul class="nav nav-pills nav-stacked">
|
||
<li><a href="#section-background-information">Background information</a></li>
|
||
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
|
||
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
|
||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||
<li><a href="#section-other-functions">Other functions</a></li>
|
||
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
|
||
<footer>
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||
<div class="copyright">
|
||
<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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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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