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Built site for AMR@2.1.1.9112: 61f2890
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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 07 December 2024.</p>
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generated on 09 December 2024.</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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@ -143,21 +143,21 @@ 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">2024-12-07</td>
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<td align="center">2024-12-09</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">2024-12-07</td>
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<td align="center">2024-12-09</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">2024-12-07</td>
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<td align="center">2024-12-09</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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@ -76,7 +76,7 @@
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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">07 December 2024</h4>
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<h4 data-toc-skip class="date">09 December 2024</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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4
extra.js
4
extra.js
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// add doctoral titles to authors
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// add doctoral titles to authors
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function doct_tit(x) {
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function doct_tit(x) {
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if (typeof(x) != "undefined") {
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if (typeof(x) != "undefined") {
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x = x.replace(/Author, maintainer/g, "Principal maintainer");
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x = x.replace(/Author, maintainer/g, "Principal developer");
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x = x.replace(/Author, contributor/g, "Contributing maintainer");
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x = x.replace(/Author, contributor/g, "Package maintainer");
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x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
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x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
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// contributors
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// contributors
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x = x.replace("Alex", "Prof. Alex");
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x = x.replace("Alex", "Prof. Alex");
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@ -11,7 +11,7 @@ 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: 2024-12-07T19:08Z
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last_built: 2024-12-09T09:33Z
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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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@ -110,16 +110,16 @@
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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 59.00546 34</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 59 59.01093 34</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.76776 19</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.77322 19</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 75 75.09836 50</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 75 75.10383 50</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.81148 52</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.81694 52</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.79781 59</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.80328 59</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.90710 11</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.91257 11</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.27869 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.28415 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.86339 21</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.86885 21</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.47268 27</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.47814 27</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.32514 13</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.33060 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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@ -785,16 +785,16 @@ 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> 2024-12-07 <span style="color: #949494;">19:09:30</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> 2024-12-09 <span style="color: #949494;">09:34:39</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> 2024-12-07 <span style="color: #949494;">19:09:38</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> 2024-12-09 <span style="color: #949494;">09:34:46</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> 2024-12-07 <span style="color: #949494;">19:09:38</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> 2024-12-09 <span style="color: #949494;">09:34:46</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> 2024-12-07 <span style="color: #949494;">19:09:39</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> 2024-12-09 <span style="color: #949494;">09:34:47</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> 2024-12-07 <span style="color: #949494;">19:09:39</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> 2024-12-09 <span style="color: #949494;">09:34:47</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> 2024-12-07 <span style="color: #949494;">19:09:30</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> 2024-12-09 <span style="color: #949494;">09:34:39</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> 2024-12-07 <span style="color: #949494;">19:09:38</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> 2024-12-09 <span style="color: #949494;">09:34:46</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> 2024-12-07 <span style="color: #949494;">19:09:38</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> 2024-12-09 <span style="color: #949494;">09:34:46</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> 2024-12-07 <span style="color: #949494;">19:09:39</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> 2024-12-09 <span style="color: #949494;">09:34:47</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> 2024-12-07 <span style="color: #949494;">19:09:39</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> 2024-12-09 <span style="color: #949494;">09:34:47</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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