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<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
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<p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e.of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e.of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
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<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 4 May 2021 13:38:27 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
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<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
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<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
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<ahref="#interpretation-from-mic-values-disk-diameters-to-rsi"class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>
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<ahref="#dosage-guidelines-from-eucast"class="anchor"></a>Dosage guidelines from EUCAST</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>