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website update since they are based on randomly created values and the
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 15 January 2025.</p>
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generated on 16 January 2025.</p>
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<div class="section level2">
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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@ -144,21 +144,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2025-01-15</td>
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<td align="center">2025-01-16</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2025-01-15</td>
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<td align="center">2025-01-16</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2025-01-15</td>
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<td align="center">2025-01-16</td>
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<td align="center">efgh</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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@ -140,7 +140,7 @@ package.</p>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span> masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span> masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span> masks <span style="color: #0000BB;">stats</span>::step()</span></span>
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<span><span class="co">#> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span> masks <span style="color: #0000BB;">stats</span>::step()</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">•</span> Dig deeper into tidy modeling with R at <span style="color: #00BB00;">https://www.tmwr.org</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">•</span> Learn how to get started at <span style="color: #00BB00;">https://www.tidymodels.org/start/</span></span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
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<span></span>
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<span></span>
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<span><span class="co"># Load the example_isolates dataset</span></span>
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<span><span class="co"># Load the example_isolates dataset</span></span>
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@ -77,7 +77,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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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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<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">15 January 2025</h4>
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<h4 data-toc-skip class="date">16 January 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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<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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<div class="d-none name"><code>datasets.Rmd</code></div>
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@ -12,7 +12,7 @@ articles:
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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welcome_to_AMR: welcome_to_AMR.html
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WHONET: WHONET.html
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WHONET: WHONET.html
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last_built: 2025-01-15T15:21Z
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last_built: 2025-01-16T11:00Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR/reference
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reference: https://msberends.github.io/AMR/reference
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article: https://msberends.github.io/AMR/articles
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article: https://msberends.github.io/AMR/articles
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@ -111,16 +111,16 @@
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">df</span></span></span>
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<span class="r-in"><span><span class="va">df</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
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<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 59 59.11233 34</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 59 59.11507 34</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.87671 19</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.87945 19</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 75 75.20548 50</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 75 75.20822 50</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.91781 52</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.92055 52</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.90411 59</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.90685 59</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 37 37.01370 11</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 37 37.01644 11</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.38630 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.38904 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.96986 21</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.97260 21</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.58082 27</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.58356 27</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.43288 13</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.43562 13</span>
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</code></pre></div>
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</code></pre></div>
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</div>
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</div>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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@ -786,16 +786,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-15 <span style="color: #949494;">15:22:23</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-16 <span style="color: #949494;">11:00:46</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-15 <span style="color: #949494;">15:22:31</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-15 <span style="color: #949494;">15:22:31</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-15 <span style="color: #949494;">15:22:32</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-15 <span style="color: #949494;">15:22:32</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-15 <span style="color: #949494;">15:22:23</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-16 <span style="color: #949494;">11:00:46</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-15 <span style="color: #949494;">15:22:31</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-15 <span style="color: #949494;">15:22:31</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-15 <span style="color: #949494;">15:22:32</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-15 <span style="color: #949494;">15:22:32</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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