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@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -81,7 +81,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">07 April 2025</h4>
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<h4 data-toc-skip class="date">08 April 2025</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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@ -97,9 +97,9 @@ Parquet, SPSS, and Stata. We also provide tab-separated text files that
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are machine-readable and suitable for input in any software program,
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such as laboratory information systems.</p>
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<blockquote>
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<p>If you are working in Python, be sure to use our <a href="https://msberends.github.io/AMR/articles/AMR_for_Python.html">AMR
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for Python</a> package. It allows all relevant AMR data sets to be
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natively available in Python.</p>
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<p>If you are working in Python, be sure to use our <a href="https://amr-for-r.org/articles/AMR_for_Python.html">AMR for
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Python</a> package. It allows all relevant AMR data sets to be natively
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available in Python.</p>
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</blockquote>
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<div class="section level2">
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<h2 id="microorganisms-full-microbial-taxonomy">
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@ -117,8 +117,8 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
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<p>This data set is in R available as <code>microorganisms</code>, after
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you load the <code>AMR</code> package.</p>
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<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.html">data
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set here</a>.</p>
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.html">data set
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.rds" class="external-link">original
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@ -425,8 +425,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
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<p>This data set is in R available as <code>antimicrobials</code>, after
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you load the <code>AMR</code> package.</p>
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<p>It was last updated on 19 March 2025 15:05:24 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">data
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set here</a>.</p>
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
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@ -602,7 +602,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
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<p>This data set is in R available as <code>clinical_breakpoints</code>,
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after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 13 March 2025 14:38:39 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">data
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
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set here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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@ -789,7 +789,7 @@ column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
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<code>microorganisms.groups</code>, after you load the <code>AMR</code>
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package.</p>
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<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">data
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.groups.html">data
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set here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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@ -878,8 +878,8 @@ column names:<br><em>mo</em> and <em>ab</em>.</p>
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<p>This data set is in R available as <code>intrinsic_resistant</code>,
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after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 28 March 2025 10:17:49 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">data
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set here</a>.</p>
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.rds" class="external-link">original
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@ -1153,7 +1153,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
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<p>This data set is in R available as <code>dosage</code>, after you
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load the <code>AMR</code> package.</p>
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<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/dosage.html">data set
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.html">data set
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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@ -1290,8 +1290,8 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
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<p>This data set is in R available as <code>example_isolates</code>,
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after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 15 June 2024 13:33:49 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/example_isolates.html">data
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set here</a>.</p>
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
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here</a>.</p>
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<p><strong>Example content</strong></p>
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<table class="table">
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<colgroup>
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@ -1695,7 +1695,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
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<code>example_isolates_unclean</code>, after you load the
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<code>AMR</code> package.</p>
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<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">data
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates_unclean.html">data
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set here</a>.</p>
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<p><strong>Example content</strong></p>
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<table style="width:100%;" class="table">
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@ -1792,7 +1792,7 @@ column names:<br><em>code</em> and <em>mo</em>.</p>
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<p>This data set is in R available as <code>microorganisms.codes</code>,
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after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">data
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
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set here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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@ -1863,8 +1863,8 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
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<p>This data set is in R available as <code>antivirals</code>, after you
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load the <code>AMR</code> package.</p>
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<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
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about the contents, (scientific) source, and structure of this <a href="https://msberends.github.io/AMR/reference/antimicrobials.html">data
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set here</a>.</p>
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about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
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here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.rds" class="external-link">original
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