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566 lines
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566 lines
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</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>
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<a href="../articles/Predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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<a href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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<a href="../articles/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="../articles/ab_property.html">
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Get properties of an antibiotic
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<a href="../articles/freq.html">
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Create frequency tables
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Use the G-test
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Other: benchmarks
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Manual
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Authors
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Changelog
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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="ITIS.html">ITIS</a></code> </p>
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</td>
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<td><p>ITIS: Integrated Taxonomic Information System</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.atc.html">as.atc()</a></code> <code><a href="as.atc.html">guess_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.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> </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="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</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="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,</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_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_subkingdom()</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_TSN()</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_taxonomy()</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_property()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_official()</a></code> <code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_trivial_nl()</a></code> <code><a href="ab_property.html">ab_certe()</a></code> <code><a href="ab_property.html">ab_umcg()</a></code> <code><a href="ab_property.html">ab_tradenames()</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="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_groups()</a></code> <code><a href="atc_property.html">atc_ddd()</a></code> </p>
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</td>
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<td><p>Properties of an ATC code</p></td>
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||
</tr><tr>
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<td>
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<p><code><a href="abname.html">abname()</a></code> </p>
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||
</td>
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<td><p>Name of an antibiotic</p></td>
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||
</tr><tr>
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||
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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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||
|
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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>
|
||
|
||
<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>
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||
</td>
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||
<td><p>Join a table with <code>microorganisms</code></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-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
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||
<p class="section-desc"><p>Functions for conducting AMR analysis</p></p>
|
||
</th>
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||
</tr>
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||
<tr>
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|
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<td>
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<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>
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</td>
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<td><p>Count isolates</p></td>
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||
</tr><tr>
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|
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<td>
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<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>
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||
</td>
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<td><p>Calculate resistance of isolates</p></td>
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</tr><tr>
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<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 bar plots with <code>ggplot</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> </p>
|
||
</td>
|
||
<td><p>Predict antimicrobial resistance</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="rsi.html">rsi()</a></code> </p>
|
||
</td>
|
||
<td><p>Calculate resistance of isolates</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 423 antibiotics</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with taxonomic data from ITIS</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="septic_patients.html">septic_patients</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with 2000 blood culture isolates of septic patients</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.certe.html">microorganisms.certe</a></code> </p>
|
||
</td>
|
||
<td><p>Translation table for Certe</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with old taxonomic data from ITIS</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.umcg.html">microorganisms.umcg</a></code> </p>
|
||
</td>
|
||
<td><p>Translation table for UMCG</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
|
||
</td>
|
||
<td><p>Supplementary Data</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-other" class="hasAnchor"><a href="#section-other" class="anchor"></a>Other</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="get_locale.html">get_locale()</a></code> </p>
|
||
</td>
|
||
<td><p>Get language for AMR</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><tr>
|
||
|
||
<td>
|
||
<p><code><a href="mo_failures.html">mo_failures()</a></code> </p>
|
||
</td>
|
||
<td><p>Vector of failed coercion attempts</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="mo_renamed.html">mo_renamed()</a></code> </p>
|
||
</td>
|
||
<td><p>Vector of taxonomic renamed items</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">Other</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
|
||
<footer>
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||
<div class="copyright">
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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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<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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