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<h1>Reference</h1>
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<col class="alias" />
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<th colspan="2">
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
<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 EUCAST rules.</p></p>
</th>
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<tr>
<td>
<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>
</td>
<td><p>Transform to ATC code</p></td>
</tr><tr>
<td>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
</td>
<td><p>Class 'mic'</p></td>
</tr><tr>
<td>
<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">guess_mo()</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></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><p>Class 'rsi'</p></td>
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<td>
<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><p>EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
</td>
<td><p>Read data from 4D database</p></td>
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</tbody><tbody>
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<th colspan="2">
<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>
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates,</p></p>
</th>
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<td>
<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>
</td>
<td><p>Determine first (weighted) isolates</p></td>
</tr><tr>
<td>
<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>
</td>
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
</tr><tr>
<td>
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
</td>
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
</tr><tr>
<td>
<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>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>
<td>
<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>
</td>
<td><p>Property of an antibiotic</p></td>
</tr><tr>
<td>
<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>
</td>
<td><p>Properties of an ATC code</p></td>
</tr><tr>
<td>
<p><code><a href="abname.html">abname()</a></code> </p>
</td>
<td><p>Name of an antibiotic</p></td>
</tr><tr>
<td>
<p><code><a href="age.html">age()</a></code> </p>
</td>
<td><p>Age in years of individuals</p></td>
</tr><tr>
<td>
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
</td>
<td><p>Split ages into age groups</p></td>
</tr><tr>
<td>
<p><code><a href="p.symbol.html">p.symbol()</a></code> </p>
</td>
<td><p>Symbol of a p value</p></td>
</tr><tr>
<td>
<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>
</tbody><tbody>
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<th colspan="2">
<h2 id="section-analysing-the-data" class="hasAnchor"><a href="#section-analysing-the-data" class="anchor"></a>Analysing the data</h2>
<p class="section-desc"><p>Functions for conducting AMR analysis</p></p>
</th>
</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="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>&lt;frequency_tbl&gt;</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>
</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>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<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-the-data">Analysing the data</a></li>
<li><a href="#section-included-data-sets">Included data sets</a></li>
<li><a href="#section-other">Other</a></li>
</ul>
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