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@ -205,14 +205,12 @@ Content not found. Please use links in the navbar.
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<footer><div class="copyright">
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<p></p>
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<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
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Erwin E. A. Hassing.</p>
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<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<div class="pkgdown">
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<p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
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2.0.2.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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@ -416,13 +416,11 @@ END OF TERMS AND CONDITIONS
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<footer><div class="copyright">
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
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Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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</div>
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<div class="pkgdown">
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
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2.0.2.</p>
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
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// v0.0.1
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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</div>
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</header><div class="row">
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</header><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>How to apply EUCAST rules</h1>
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<div class="pkgdown">
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<p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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</div>
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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
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// v0.0.1
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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document.addEventListener('DOMContentLoaded', function() {
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const codeList = document.getElementsByClassName("sourceCode");
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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</div>
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</header><div class="row">
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</header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
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@ -295,8 +295,8 @@
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<span class="co"># Table 3 - Enterobacteriaceae... OK.</span>
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<span class="co"># Table 4 - Pseudomonas aeruginosa... OK.</span>
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<span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
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<span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
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<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
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<span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
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<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
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<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
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<p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
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<p>(16 isolates had no test results)</p>
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@ -320,17 +320,17 @@ Unique: 2</p>
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<td align="left">1</td>
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<td align="left">Negative</td>
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<td align="right">1601</td>
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<td align="right">92.60%</td>
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<td align="right">92.6%</td>
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<td align="right">1601</td>
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<td align="right">92.60%</td>
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<td align="right">92.6%</td>
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</tr>
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<tr class="even">
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<td align="left">2</td>
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<td align="left">Multi-drug-resistant (MDR)</td>
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<td align="right">128</td>
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<td align="right">7.40%</td>
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<td align="right">7.4%</td>
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<td align="right">1729</td>
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<td align="right">100.00%</td>
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<td align="right">100.0%</td>
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</tr>
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</tbody>
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</table>
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@ -358,18 +358,18 @@ Unique: 2</p>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
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<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
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<span class="co"># 1 I R I S R S</span>
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<span class="co"># 2 I S R R S R</span>
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<span class="co"># 3 R I S I R S</span>
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<span class="co"># 4 S S I R I S</span>
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<span class="co"># 5 S R S S S I</span>
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<span class="co"># 6 S R R S R I</span>
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<span class="co"># 1 I R I R I I</span>
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<span class="co"># 2 I R I I I I</span>
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<span class="co"># 3 S I I R S S</span>
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<span class="co"># 4 R I R I R I</span>
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<span class="co"># 5 S I S S R S</span>
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<span class="co"># 6 S S I I I S</span>
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<span class="co"># kanamycin</span>
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<span class="co"># 1 S</span>
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<span class="co"># 2 I</span>
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<span class="co"># 3 R</span>
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<span class="co"># 4 R</span>
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<span class="co"># 5 I</span>
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<span class="co"># 1 I</span>
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<span class="co"># 2 R</span>
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<span class="co"># 3 I</span>
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<span class="co"># 4 I</span>
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<span class="co"># 5 R</span>
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<span class="co"># 6 R</span></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
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<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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@ -398,7 +398,7 @@ Unique: 2</p>
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<p>Class: factor > ordered (numeric)<br>
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Length: 5,000<br>
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Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <…<br>
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Available: 5,000 (100.0%, NA: 0 = 0.0%)<br>
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Available: 5,000 (100%, NA: 0 = 0%)<br>
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Unique: 5</p>
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<table class="table">
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<thead><tr class="header">
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@ -413,40 +413,40 @@ Unique: 5</p>
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">Mono-resistant</td>
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<td align="right">3250</td>
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<td align="right">65.00%</td>
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<td align="right">3250</td>
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<td align="right">65.00%</td>
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<td align="right">3243</td>
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<td align="right">64.86%</td>
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<td align="right">3243</td>
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<td align="right">64.86%</td>
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</tr>
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<tr class="even">
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<td align="left">2</td>
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<td align="left">Negative</td>
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<td align="right">975</td>
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<td align="right">19.50%</td>
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<td align="right">4225</td>
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<td align="right">84.50%</td>
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<td align="right">969</td>
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<td align="right">19.38%</td>
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<td align="right">4212</td>
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<td align="right">84.24%</td>
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</tr>
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<tr class="odd">
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<td align="left">3</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="right">474</td>
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<td align="right">9.48%</td>
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<td align="right">4699</td>
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<td align="right">93.98%</td>
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<td align="right">425</td>
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<td align="right">8.50%</td>
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<td align="right">4637</td>
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<td align="right">92.74%</td>
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</tr>
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<tr class="even">
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<td align="left">4</td>
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<td align="left">Poly-resistant</td>
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<td align="right">203</td>
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<td align="right">4.06%</td>
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<td align="right">4902</td>
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<td align="right">98.04%</td>
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<td align="right">263</td>
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<td align="right">5.26%</td>
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<td align="right">4900</td>
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<td align="right">98.00%</td>
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</tr>
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<tr class="odd">
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<td align="left">5</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="right">98</td>
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<td align="right">1.96%</td>
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<td align="right">100</td>
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<td align="right">2.00%</td>
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<td align="right">5000</td>
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<td align="right">100.00%</td>
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</tr>
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<div class="pkgdown">
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<p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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</div>
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</footer>
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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
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// v0.0.1
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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document.addEventListener('DOMContentLoaded', function() {
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const codeList = document.getElementsByClassName("sourceCode");
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for (var i = 0; i < codeList.length; i++) {
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var linkList = codeList[i].getElementsByTagName('a');
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}
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}
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});
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
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</span>
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</div>
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</header><div class="row">
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</header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
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@ -199,18 +199,18 @@
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<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
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<div class="section level1">
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<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h1>
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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>
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</div>
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<div class="section level1">
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<h1 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
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</h1>
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<div class="section level2">
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<h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
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</h2>
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<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><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>
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<code class="sourceCode R"><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>
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<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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
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<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
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<span class="co"># Rows: 2,000</span>
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<span class="co"># Columns: 49</span>
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<span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
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<span class="co"># <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="co"># <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level1">
|
||||
<h1 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||||
</h2>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">pca_result</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
|
||||
|
|
@ -305,9 +305,9 @@
|
|||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></code></pre>
|
||||
<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||||
</div>
|
||||
<div class="section level1">
|
||||
<h1 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||||
</h2>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||||
|
|
@ -340,7 +340,7 @@
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
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|
@ -0,0 +1,15 @@
|
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// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
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if (linkList[j].innerHTML === "") {
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@ -44,7 +44,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -185,13 +185,13 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">23 December 2021</h4>
|
||||
<h4 data-toc-skip class="date">12 March 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
|
|
@ -226,7 +226,7 @@
|
|||
</li>
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">430,288 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,030 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||
|
|
@ -241,7 +241,7 @@
|
|||
<li>
|
||||
<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
|
||||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
</li>
|
||||
</ul>
|
||||
<p>To demonstrate the first point:</p>
|
||||
|
|
@ -414,7 +414,7 @@
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,15 @@
|
|||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
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|
||||
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|
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|
||||
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|
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|
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|
||||
}
|
||||
});
|
||||
|
|
@ -44,7 +44,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -185,7 +185,7 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to work with WHONET data</h1>
|
||||
|
|
@ -215,7 +215,7 @@
|
|||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</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://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</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"># this package</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"># this package</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://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
|
||||
<p>We will have to transform some variables to simplify and automate the analysis:</p>
|
||||
<ul>
|
||||
|
|
@ -238,7 +238,7 @@
|
|||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 500<br>
|
||||
Available: 500 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Available: 500 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 37</p>
|
||||
<p>Shortest: 11<br>
|
||||
Longest: 40</p>
|
||||
|
|
@ -334,7 +334,7 @@ Longest: 40</p>
|
|||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>(omitted 27 entries, n = 56 [11.20%])</p>
|
||||
<p>(omitted 27 entries, n = 56 [11.2%])</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># our transformed antibiotic columns</span>
|
||||
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
|
||||
|
|
@ -413,7 +413,7 @@ Drug group: Beta-lactams/penicillins<br>
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,15 @@
|
|||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
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|
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|
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|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -185,7 +185,7 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
|
|
@ -202,7 +202,7 @@
|
|||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><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://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</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="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="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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
|
||||
|
|
@ -222,23 +222,23 @@
|
|||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25</span>
|
||||
<span class="co"># as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25</span>
|
||||
<span class="co"># as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25</span>
|
||||
<span class="co"># as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25</span>
|
||||
<span class="co"># as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 20.0 20.0 25.0 20.0 21 57 25</span>
|
||||
<span class="co"># as.mo("stau") 94.0 94.0 110.0 95.0 130 130 25</span>
|
||||
<span class="co"># as.mo("STAU") 94.0 95.0 110.0 130.0 130 130 25</span>
|
||||
<span class="co"># as.mo("staaur") 20.0 20.0 28.0 20.0 21 58 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 20.0 20.0 25.0 20.0 21 57 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 56.0 56.0 72.0 57.0 92 97 25</span>
|
||||
<span class="co"># as.mo("S aureus") 55.0 56.0 66.0 56.0 75 93 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 5.7 5.8 7.3 5.9 6 41 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 370.0 370.0 390.0 380.0 410 410 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 260.0 290.0 300.0 290.0 300 330 25</span>
|
||||
<span class="co"># as.mo("MRSA") 20.0 20.0 23.0 20.0 20 56 25</span>
|
||||
<span class="co"># as.mo("VISA") 34.0 35.0 48.0 35.0 35 220 25</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.</p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 65 times slower to determine.</p>
|
||||
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||
|
|
@ -258,8 +258,8 @@
|
|||
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># Class <mo></span>
|
||||
<span class="co"># [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS</span>
|
||||
<span class="co"># [6] B_CRYNB_STRT</span>
|
||||
<span class="co"># [1] B_PROTS_MRBL B_STPHY_CONS B_ESCHR_COLI B_PSDMN_AERG B_ENTRC_FCLS</span>
|
||||
<span class="co"># [6] B_STPHY_AURS</span>
|
||||
|
||||
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
|
|
@ -272,11 +272,11 @@
|
|||
<span class="co"># now let's see:</span>
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 196 209 274 223 364 388 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 265 269 357 298 471 516 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.298 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||
|
|
@ -287,13 +287,13 @@
|
|||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 8.00 9.16 9.19 9.28 9.46 9.73 10</span>
|
||||
<span class="co"># B 23.40 27.20 32.60 27.90 28.10 80.20 10</span>
|
||||
<span class="co"># C 1.85 2.25 2.40 2.47 2.62 2.90 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 12.30 12.30 12.60 12.50 12.60 14.2 10</span>
|
||||
<span class="co"># B 61.70 61.90 62.70 62.40 62.50 66.2 10</span>
|
||||
<span class="co"># C 3.04 3.05 6.92 3.12 3.21 40.9 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0031 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
|
|
@ -304,17 +304,17 @@
|
|||
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
||||
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.76 1.80 2.07 1.95 2.26 2.90 10</span>
|
||||
<span class="co"># B 1.69 1.73 1.90 1.81 2.03 2.48 10</span>
|
||||
<span class="co"># C 1.71 1.77 1.92 1.91 2.05 2.17 10</span>
|
||||
<span class="co"># D 1.68 1.71 1.76 1.76 1.82 1.88 10</span>
|
||||
<span class="co"># E 1.68 1.70 1.89 1.89 2.04 2.26 10</span>
|
||||
<span class="co"># F 1.67 1.75 1.93 1.89 2.11 2.35 10</span>
|
||||
<span class="co"># G 1.70 1.76 1.97 1.88 2.12 2.43 10</span>
|
||||
<span class="co"># H 1.67 1.71 1.83 1.75 1.98 2.14 10</span></code></pre></div>
|
||||
<span class="co"># A 3.02 3.09 3.22 3.10 3.46 3.55 10</span>
|
||||
<span class="co"># B 3.03 3.04 3.21 3.12 3.42 3.48 10</span>
|
||||
<span class="co"># C 3.03 3.05 3.08 3.06 3.12 3.16 10</span>
|
||||
<span class="co"># D 2.98 3.01 3.17 3.09 3.40 3.47 10</span>
|
||||
<span class="co"># E 3.01 3.06 3.19 3.12 3.43 3.43 10</span>
|
||||
<span class="co"># F 2.95 2.99 3.11 3.05 3.16 3.46 10</span>
|
||||
<span class="co"># G 2.94 3.06 3.19 3.13 3.41 3.54 10</span>
|
||||
<span class="co"># H 2.93 3.01 3.12 3.08 3.19 3.42 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
|
|
@ -347,19 +347,19 @@
|
|||
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
|
||||
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100</span>
|
||||
<span class="co"># de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100</span>
|
||||
<span class="co"># en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100</span>
|
||||
<span class="co"># es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100</span>
|
||||
<span class="co"># fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100</span>
|
||||
<span class="co"># it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100</span>
|
||||
<span class="co"># nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100</span>
|
||||
<span class="co"># pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100</span>
|
||||
<span class="co"># ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100</span>
|
||||
<span class="co"># sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># da 3.579 3.689 3.811 3.737 3.894 4.626 100</span>
|
||||
<span class="co"># de 3.600 3.694 4.205 3.750 3.869 43.820 100</span>
|
||||
<span class="co"># en 1.686 1.720 1.828 1.766 1.822 2.244 100</span>
|
||||
<span class="co"># es 3.618 3.688 4.633 3.772 4.083 43.890 100</span>
|
||||
<span class="co"># fr 3.493 3.602 4.104 3.658 3.785 41.860 100</span>
|
||||
<span class="co"># it 3.543 3.628 4.152 3.702 3.810 44.040 100</span>
|
||||
<span class="co"># nl 3.625 3.716 5.024 3.763 3.924 44.220 100</span>
|
||||
<span class="co"># pt 3.510 3.610 3.742 3.684 3.861 4.096 100</span>
|
||||
<span class="co"># ru 3.568 3.680 4.534 3.742 3.871 41.170 100</span>
|
||||
<span class="co"># sv 3.585 3.664 3.833 3.748 4.046 4.987 100</span></code></pre></div>
|
||||
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -379,7 +379,7 @@
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,15 @@
|
|||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
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|
||||
if (linkList[j].innerHTML === "") {
|
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linkList[j].setAttribute('aria-hidden', 'true');
|
||||
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|
||||
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|
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|
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});
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 81 KiB After Width: | Height: | Size: 76 KiB |
|
|
@ -185,12 +185,12 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">10 March 2022</h4>
|
||||
<h4 data-toc-skip class="date">12 March 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
|
|
@ -199,71 +199,42 @@
|
|||
|
||||
|
||||
|
||||
<p>All reference data (about microorganisms, antibiotics, R/SI
|
||||
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
||||
reliable, up-to-date and freely available. We continually export our
|
||||
data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
|
||||
supply tab separated files that are machine-readable and suitable for
|
||||
input in any software program, such as laboratory information
|
||||
systems.</p>
|
||||
<p>On this page, we explain how to download them and how the structure
|
||||
of the data sets look like.</p>
|
||||
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
|
||||
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
|
||||
<p class="dataset-within-r">
|
||||
If you are reading this page from within R, please
|
||||
<a href="https://msberends.github.io/AMR/articles/datasets.html">visit
|
||||
our website</a>, which is automatically updated with every code change.
|
||||
If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
|
||||
</p>
|
||||
<div class="section level2">
|
||||
<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
|
||||
</h2>
|
||||
<p>A data set with 70,760 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 29 November 2021 11:38:23 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p>A data set with 70,760 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 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
|
||||
file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
|
||||
file</a> (6.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
|
||||
text file</a> (13.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
|
||||
file</a> (30.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS
|
||||
file</a> (16.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
|
||||
file</a> (27.5 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
|
||||
</ul>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not
|
||||
contain SNOMED codes, as their file size would exceed 100 MB; the file
|
||||
size limit of GitHub.</strong> Advice? Use R instead.</p>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
|
||||
</h3>
|
||||
<p>Our full taxonomy of microorganisms is based on the authoritative and
|
||||
comprehensive:</p>
|
||||
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
|
||||
(included version: 2019)</li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
|
||||
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public
|
||||
Health Information Network Vocabulary Access and Distribution System
|
||||
(PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
|
|
@ -456,64 +427,40 @@ Health Information Network Vocabulary Access and Distribution System
|
|||
<div class="section level2">
|
||||
<h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
|
||||
</h2>
|
||||
<p>A data set with 14,338 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 6 October 2021 14:38:29 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p>A data set with 14,338 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 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
|
||||
file</a> (0.2 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel
|
||||
file</a> (0.5 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain
|
||||
text file</a> (1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS
|
||||
file</a> (2.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS
|
||||
file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata
|
||||
file</a> (2 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
|
||||
</h3>
|
||||
<p>This data set contains old, previously accepted taxonomic names. The
|
||||
data sources are the same as the <code>microorganisms</code> data
|
||||
set:</p>
|
||||
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
|
||||
(included version: 2019)</li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
|
||||
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
|
||||
</h3>
|
||||
<p>Example rows when filtering on <em>Escherichia</em>:</p>
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="31%">
|
||||
<col width="30%">
|
||||
<col width="24%">
|
||||
<col width="13%">
|
||||
</colgroup>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">fullname</th>
|
||||
<th align="center">fullname_new</th>
|
||||
|
|
@ -546,50 +493,31 @@ Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
|||
<div class="section level2">
|
||||
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
|
||||
</h2>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following
|
||||
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</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 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</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 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R
|
||||
file</a> (33 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel
|
||||
file</a> (65 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain
|
||||
text file</a> (0.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
|
||||
file</a> (1.8 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS
|
||||
file</a> (0.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
|
||||
file</a> (0.3 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
|
||||
</h3>
|
||||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO
|
||||
and WHONET, and all compound IDs from PubChem. It also contains all
|
||||
brand names (synonyms) as found on PubChem and Defined Daily Doses
|
||||
(DDDs) for oral and parenteral administration.</p>
|
||||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
|
||||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||||
not be used for commercial purposes, but is freely available from the
|
||||
WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||||
National Library of Medicine</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
|
@ -669,8 +597,7 @@ National Library of Medicine</a></li>
|
|||
<td align="center">Beta-lactams/penicillins</td>
|
||||
<td align="center">J01CR02</td>
|
||||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||||
<td align="center">Combinations of penicillins, incl. beta-lactamase
|
||||
inhibitors</td>
|
||||
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
|
||||
<td align="center">a/c, amcl, aml, …</td>
|
||||
<td align="center">amocla, amoclan, amoclav, …</td>
|
||||
<td align="center">1.5</td>
|
||||
|
|
@ -734,49 +661,31 @@ inhibitors</td>
|
|||
<div class="section level2">
|
||||
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
|
||||
</h2>
|
||||
<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 29 August 2020 19:53:07 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<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 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R
|
||||
file</a> (5 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel
|
||||
file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain
|
||||
text file</a> (16 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
|
||||
file</a> (80 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS
|
||||
file</a> (68 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
|
||||
file</a> (67 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
|
||||
</h3>
|
||||
<p>This data set contains all ATC codes gathered from WHO and all
|
||||
compound IDs from PubChem. It also contains all brand names (synonyms)
|
||||
as found on PubChem and Defined Daily Doses (DDDs) for oral and
|
||||
parenteral administration.</p>
|
||||
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
|
||||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||||
not be used for commercial purposes, but is freely available from the
|
||||
WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||||
National Library of Medicine</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
|
|
@ -810,8 +719,7 @@ National Library of Medicine</a></li>
|
|||
<td align="center">J05AF06</td>
|
||||
<td align="center">441300</td>
|
||||
<td align="center">Abacavir</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||||
inhibitors</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||||
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
|
||||
<td align="center">0.6</td>
|
||||
<td align="center">g</td>
|
||||
|
|
@ -822,8 +730,7 @@ inhibitors</td>
|
|||
<td align="center">J05AB01</td>
|
||||
<td align="center">135398513</td>
|
||||
<td align="center">Aciclovir</td>
|
||||
<td align="center">Nucleosides and nucleotides excl. reverse
|
||||
transcriptase inhibitors</td>
|
||||
<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
|
||||
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
|
||||
<td align="center">4.0</td>
|
||||
<td align="center">g</td>
|
||||
|
|
@ -834,10 +741,8 @@ transcriptase inhibitors</td>
|
|||
<td align="center">J05AF08</td>
|
||||
<td align="center">60871</td>
|
||||
<td align="center">Adefovir dipivoxil</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||||
inhibitors</td>
|
||||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir
|
||||
Dipivoxil, …</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
|
||||
<td align="center">10.0</td>
|
||||
<td align="center">mg</td>
|
||||
<td align="center"></td>
|
||||
|
|
@ -883,39 +788,27 @@ Dipivoxil, …</td>
|
|||
<div class="section level2">
|
||||
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following
|
||||
column names:<br><em>mo</em> and <em>ab</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 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</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 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R
|
||||
file</a> (78 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
|
||||
file</a> (0.9 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
|
||||
text file</a> (5.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
|
||||
file</a> (10.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS
|
||||
file</a> (7.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
|
||||
file</a> (10.2 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
</h3>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of
|
||||
all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST
|
||||
Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
|
||||
v3.3</a> (2021).</p>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
|
||||
|
|
@ -1162,40 +1055,27 @@ v3.3</a> (2021).</p>
|
|||
<div class="section level2">
|
||||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||||
</h2>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following
|
||||
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
|
||||
<em>rank_index</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 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</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 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
|
||||
file</a> (39 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
|
||||
file</a> (0.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
|
||||
text file</a> (1.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
|
||||
file</a> (3.6 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
|
||||
file</a> (2.2 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
|
||||
file</a> (3.4 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||||
</h3>
|
||||
<p>This data set contains interpretation rules for MIC values and disk
|
||||
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
||||
(2011-2021).</p>
|
||||
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
|
||||
|
|
@ -1313,57 +1193,33 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
|||
<div class="section level2">
|
||||
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
|
||||
</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 25 January 2021 20:58:20 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<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 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R
|
||||
file</a> (3 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel
|
||||
file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain
|
||||
text file</a> (15 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
|
||||
file</a> (52 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS
|
||||
file</a> (45 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
|
||||
file</a> (44 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
|
||||
</h3>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in
|
||||
this data set.</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
|
||||
Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="4%">
|
||||
<col width="10%">
|
||||
<col width="15%">
|
||||
<col width="10%">
|
||||
<col width="9%">
|
||||
<col width="13%">
|
||||
<col width="5%">
|
||||
<col width="16%">
|
||||
<col width="13%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">ab</th>
|
||||
<th align="center">name</th>
|
||||
|
|
@ -1460,14 +1316,12 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
|
|||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
|
|
@ -185,13 +185,11 @@
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -185,7 +185,7 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
|
||||
|
|
@ -206,7 +206,7 @@
|
|||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</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://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</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="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"># (if not yet installed, install with:)</span>
|
||||
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></code></pre></div>
|
||||
|
|
@ -216,18 +216,18 @@
|
|||
</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot"><-</span> example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP <-<span class="st"> </span>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a> <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
|
||||
|
|
@ -264,7 +264,8 @@
|
|||
<span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span>
|
||||
<span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span>
|
||||
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
|
||||
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></code></pre></div>
|
||||
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span>
|
||||
<span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
|
||||
|
|
@ -371,7 +372,7 @@
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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|
||||
</footer>
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|
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@ -0,0 +1,15 @@
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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@ -44,7 +44,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -185,7 +185,7 @@
|
|||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
|
||||
|
|
@ -242,7 +242,7 @@
|
|||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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</div>
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</footer>
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@ -0,0 +1,15 @@
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// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
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// v0.0.1
|
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// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
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document.addEventListener('DOMContentLoaded', function() {
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const codeList = document.getElementsByClassName("sourceCode");
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});
|
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|
|
@ -269,13 +269,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
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2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
330
docs/index.html
330
docs/index.html
|
|
@ -195,75 +195,22 @@
|
|||
<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
|
||||
</h1></div>
|
||||
<blockquote>
|
||||
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||||
guideline for intrinsic resistance</a> (v3.3, October 2021) is now
|
||||
supported, the CLSI 2021 interpretation guideline is now supported, and
|
||||
our taxonomy tables have been updated as well (LPSN, 5 October
|
||||
2021).</p>
|
||||
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).</p>
|
||||
</blockquote>
|
||||
<div class="section level3">
|
||||
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
|
||||
</h3>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
|
||||
of Antimicrobial Resistance (AMR) and to work with microbial and
|
||||
antimicrobial data and properties, by using evidence-based methods.
|
||||
<strong>Our aim is to provide a standard</strong> for clean and
|
||||
reproducible AMR data analysis, that can therefore empower
|
||||
epidemiological analyses to continuously enable surveillance and
|
||||
treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
|
||||
microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
|
||||
and antiviral drugs</strong></a> by name and code (including ATC,
|
||||
WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
|
||||
valid R/SI and MIC values. It supports any data format, including
|
||||
WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in
|
||||
<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Danish,
|
||||
<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Dutch,
|
||||
<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
English,
|
||||
<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
French,
|
||||
<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
German,
|
||||
<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Italian,
|
||||
<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Portuguese,
|
||||
<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Russian,
|
||||
<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Spanish and
|
||||
<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Swedish. Antimicrobial drug (group) names and colloquial microorganism
|
||||
names are provided in these languages.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
|
||||
of any other R package</a> and works on Windows, macOS and Linux with
|
||||
all versions of R since R-3.0 (April 2013). <strong>It was designed to
|
||||
work in any setting, including those with very limited
|
||||
resources</strong>. It was created for both routine data analysis and
|
||||
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
|
||||
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
|
||||
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
|
||||
R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||||
10.33612/diss.192486375</a>) but is <a href="./news">actively and
|
||||
durably maintained</a> by two public healthcare organisations in the
|
||||
Netherlands.</p>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
|
||||
<strong>Used in 175 countries</strong><br> Since its first public
|
||||
release in early 2018, this R package has been used in almost all
|
||||
countries in the world. Click the map to enlarge and to see the country
|
||||
names.
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
|
||||
</p>
|
||||
</div>
|
||||
<div class="section level5">
|
||||
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable
|
||||
microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
|
||||
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
|
||||
</h5>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
|
||||
|
|
@ -277,12 +224,7 @@ microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-am
|
|||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
|
||||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>With only having defined a row filter on Gram-negative bacteria with
|
||||
intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
|
||||
and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
|
||||
two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
|
||||
<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
|
||||
<code>AMR</code> package make sure you get what you meant:</p>
|
||||
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">bacteria</th>
|
||||
|
|
@ -396,14 +338,9 @@ two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html"
|
|||
<div class="section level4">
|
||||
<h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
|
||||
</h4>
|
||||
<p>The development of this package is part of, related to, or made
|
||||
possible by:</p>
|
||||
<p>The development of this package is part of, related to, or made possible by:</p>
|
||||
<div align="center">
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
|
||||
<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
|
||||
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
|
||||
<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
|
||||
<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -412,33 +349,21 @@ possible by:</p>
|
|||
</h3>
|
||||
<p>This package can be used for:</p>
|
||||
<ul>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package
|
||||
contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
|
||||
Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest
|
||||
CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of
|
||||
administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||||
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
|
||||
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
|
||||
organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and
|
||||
combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models
|
||||
(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species,
|
||||
genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of
|
||||
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a
|
||||
microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an
|
||||
antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
|
||||
translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
|
||||
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
|
@ -449,24 +374,17 @@ translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/d
|
|||
<h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
|
||||
</h4>
|
||||
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R
|
||||
network (CRAN)</a>. Install this package in R from CRAN by using the
|
||||
command:</p>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click
|
||||
on the menu <em>Tools</em> > <em>Install Packages…</em> and then type
|
||||
in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be
|
||||
available in this latest release. To use all functions and data sets
|
||||
mentioned on this website, install the latest development version.</p>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
|
||||
</h4>
|
||||
<p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
|
||||
<p>The latest and unpublished development version can be installed from
|
||||
GitHub in two ways:</p>
|
||||
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>
|
||||
<p>Manually, using:</p>
|
||||
|
|
@ -475,16 +393,11 @@ GitHub in two ways:</p>
|
|||
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe
|
||||
platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
|
||||
R-universe address</a> to your list of repositories (‘repos’):</p>
|
||||
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
|
||||
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>After this, you can install and update this <code>AMR</code> package
|
||||
like any official release (e.g., using
|
||||
<code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
|
||||
> <em>Check for Package Updates…</em>).</p>
|
||||
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> > <em>Check for Package Updates…</em>).</p>
|
||||
</li>
|
||||
</ol>
|
||||
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
|
||||
|
|
@ -493,8 +406,7 @@ like any official release (e.g., using
|
|||
<div class="section level3">
|
||||
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
|
||||
</h3>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
|
||||
click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
|
||||
|
|
@ -502,181 +414,66 @@ click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How t
|
|||
<div class="section level4">
|
||||
<h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains the complete taxonomic tree of almost all
|
||||
~70,000 microorganisms from the authoritative and comprehensive
|
||||
Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
|
||||
supplemented by data from the List of Prokaryotic names with Standing in
|
||||
Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
|
||||
This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
|
||||
which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
|
||||
checked which version of the CoL is included in this package.</p>
|
||||
<p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
|
||||
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains <strong>all ~550 antibiotic, antimycotic and
|
||||
antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
|
||||
codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
|
||||
World Health Organization Collaborating Centre for Drug Statistics
|
||||
Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
|
||||
Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
|
||||
purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
|
||||
</h4>
|
||||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can
|
||||
be imported into R and can be analysed easily using this package. For
|
||||
education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
|
||||
with the exact same structure as a WHONET export file. Furthermore, this
|
||||
package also contains a <a href="./reference/antibiotics.html">data set
|
||||
antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
|
||||
almost all WHONET abbreviations for microorganisms. When using WHONET
|
||||
data as input for analysis, all input parameters will be set
|
||||
automatically.</p>
|
||||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
|
||||
with WHONET data here</a>.</p>
|
||||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
|
||||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
|
||||
</h4>
|
||||
<p>The <code>AMR</code> package basically does four important
|
||||
things:</p>
|
||||
<p>The <code>AMR</code> package basically does four important things:</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new
|
||||
<em>classes</em> for microoganisms, antibiotics and antimicrobial
|
||||
results (both S/I/R and MIC). By installing this package, you teach R
|
||||
everything about microbiology that is needed for analysis. These
|
||||
functions all use intelligent rules to guess results that you would
|
||||
expect:</p>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
|
||||
readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
|
||||
is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
|
||||
aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
|
||||
input that looks like the name or code of a microorganism like “E.
|
||||
coli”, “esco” or “esccol” and tries to find expected results using
|
||||
intelligent rules combined with the included Catalogue of Life data set.
|
||||
It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
|
||||
<em>Staphylococci</em> into coagulase negative and positive (CoNS and
|
||||
CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
|
||||
categorise <em>Streptococci</em> into Lancefield groups (like
|
||||
beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
|
||||
IDs, these IDs are also human readable based on those used by EARS-Net.
|
||||
For example, the ID of amoxicillin is <code>AMX</code> and the ID of
|
||||
gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
|
||||
uses intelligent rules to find results like accepting misspelling, trade
|
||||
names and abbrevations used in many laboratory systems. For instance,
|
||||
the values “Furabid”, “Furadantin”, “nitro” all return the ID of
|
||||
Nitrofurantoine. To accomplish this, the package contains a database
|
||||
with most LIS codes, official names, trade names, ATC codes, defined
|
||||
daily doses (DDD) and drug categories of antibiotics.</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
|
||||
raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
|
||||
existing values to valid antimicrobial results. It produces just S, I or
|
||||
R based on your input and warns about invalid values. Even values like
|
||||
“<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
|
||||
so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
|
||||
as levels. A value like “<=0.002; S” (combined MIC/RSI) will result
|
||||
in “<=0.002”.</li>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>enhances existing data</strong> and <strong>adds new
|
||||
data</strong> from data sets included in this package.</p>
|
||||
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||||
expert rules to isolates</a> (not the translation from MIC to R/SI
|
||||
values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
|
||||
every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
|
||||
guidelines from the CLSI</a> (Clinical and Laboratory Standards
|
||||
Institute).
|
||||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
|
||||
<ul>
|
||||
<li>You can also identify first <em>weighted</em> isolates of every
|
||||
patient, an adjusted version of the CLSI guideline. This takes into
|
||||
account key antibiotics of every strain and compares them.</li>
|
||||
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
|
||||
multi-drug resistant organisms (MDRO). It supports a variety of
|
||||
international guidelines, such as the MDR-paper by Magiorakos <em>et
|
||||
al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
|
||||
21793988</a>), the exceptional phenotype definitions of EUCAST and the
|
||||
WHO guideline on multi-drug resistant TB. It also supports the national
|
||||
guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set
|
||||
microorganisms</a> contains the complete taxonomic tree of ~70,000
|
||||
microorganisms. Furthermore, some colloquial names and all Gram stains
|
||||
are available, which enables resistance analysis of e.g. different
|
||||
antibiotics per Gram stain. The package also contains functions to look
|
||||
up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
|
||||
<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
|
||||
<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
|
||||
SNOMED CT code associated with a microorganism. As all these function
|
||||
use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
|
||||
rules for determination. For example, <code>mo_genus("MRSA")</code> and
|
||||
<code>mo_genus("S. aureus")</code> will both return
|
||||
<code>"Staphylococcus"</code>. They also come with support for German,
|
||||
Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
|
||||
can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
|
||||
contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
|
||||
PubChem compound ID, LOINC code, official name, common LIS codes and
|
||||
DDDs of both oral and parenteral administration. It also contains all
|
||||
(thousands of) trade names found in PubChem. Use functions like
|
||||
<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
|
||||
<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
|
||||
values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
|
||||
internally so they support the same intelligent rules to guess the most
|
||||
probable result. For example, <code>ab_name("Fluclox")</code>,
|
||||
<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
|
||||
will all return <code>"Flucloxacillin"</code>. These functions can again
|
||||
be used to add new variables to your data.</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions
|
||||
that use well-known methods.</p>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
|
||||
<ul>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even
|
||||
co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
|
||||
<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
|
||||
<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
|
||||
<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
|
||||
<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
|
||||
isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
|
||||
<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
|
||||
All these functions can be used with the <code>dplyr</code> package
|
||||
(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
|
||||
the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using
|
||||
logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
function</li>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>teaches the user</strong> how to use all the above
|
||||
actions.</p>
|
||||
<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
|
||||
<ul>
|
||||
<li>Aside from this website with many tutorials, the package itself
|
||||
contains extensive help pages with many examples for all functions.</li>
|
||||
<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
|
||||
<li>The package also contains example data sets:
|
||||
<ul>
|
||||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
|
||||
data set</a>. This data set contains 2,000 microbial isolates with their
|
||||
full antibiograms. It reflects reality and can be used to practice AMR
|
||||
data analysis.</li>
|
||||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
|
||||
set</a>. This data set only contains fake data, but with the exact same
|
||||
structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
|
||||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -687,9 +484,7 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
|
|||
<div class="section level3">
|
||||
<h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
|
||||
</h3>
|
||||
<p>This R package is free, open-source software and licensed under the
|
||||
<a href="./LICENSE-text.html">GNU General Public License v2.0
|
||||
(GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||||
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||||
<ul>
|
||||
<li><p>May be used for commercial purposes</p></li>
|
||||
<li><p>May be used for private purposes</p></li>
|
||||
|
|
@ -697,18 +492,15 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
|
|||
<li>
|
||||
<p>May be modified, although:</p>
|
||||
<ul>
|
||||
<li>Modifications <strong>must</strong> be released under the same
|
||||
license when distributing the package</li>
|
||||
<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
|
||||
<li>Changes made to the code <strong>must</strong> be documented</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>May be distributed, although:</p>
|
||||
<ul>
|
||||
<li>Source code <strong>must</strong> be made available when the package
|
||||
is distributed</li>
|
||||
<li>A copy of the license and copyright notice <strong>must</strong> be
|
||||
included with the package.</li>
|
||||
<li>Source code <strong>must</strong> be made available when the package is distributed</li>
|
||||
<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><p>Comes with a LIMITATION of liability</p></li>
|
||||
|
|
@ -764,14 +556,12 @@ included with the package.</li>
|
|||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -157,14 +157,15 @@
|
|||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="page-header" data-toc-text="1.8.0.9004" id="amr-1809004">
|
||||
<code>AMR</code> 1.8.0.9004<a class="anchor" aria-label="anchor" href="#amr-1809004"></a></h2>
|
||||
<h2 class="page-header" data-toc-text="1.8.0.9005" id="amr-1809005">
|
||||
<code>AMR</code> 1.8.0.9005<a class="anchor" aria-label="anchor" href="#amr-1809005"></a></h2>
|
||||
<div class="section level3">
|
||||
<h3 id="last-updated-march-1-8-0-9004"><small>Last updated: 3 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9004"></a></h3>
|
||||
<h3 id="last-updated-march-1-8-0-9005"><small>Last updated: 10 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9005"></a></h3>
|
||||
<p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-1-8-0-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9004"></a></h4>
|
||||
<ul><li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
|
||||
<h4 id="changed-1-8-0-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9005"></a></h4>
|
||||
<ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped values (such as <code>>=</code>), sometimes leading to <code>NA</code></p></li>
|
||||
<li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
|
||||
<li>
|
||||
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
|
|
@ -177,7 +178,7 @@
|
|||
<li><p>Updated MIC printing in tibbles</p></li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="other-1-8-0-9004">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9004"></a></h4>
|
||||
<h4 id="other-1-8-0-9005">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9005"></a></h4>
|
||||
<ul><li>Fix for unit testing on R 3.3</li>
|
||||
<li>Fix for size of some image elements, as requested by CRAN</li>
|
||||
</ul></div>
|
||||
|
|
@ -270,7 +271,7 @@
|
|||
</li>
|
||||
<li>Improved plot legends for MICs and disk diffusion values</li>
|
||||
<li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code> functions</li>
|
||||
<li>Added <code>fortify()</code> extensions for plotting methods</li>
|
||||
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify()</a></code> extensions for plotting methods</li>
|
||||
<li>
|
||||
<code>NA</code> values of the classes <code><mic></code>, <code><disk></code> and <code><rsi></code> are now exported objects of this package, e.g. <code>NA_mic_</code> is an <code>NA</code> of class <code>mic</code> (just like the base R <code>NA_character_</code> is an <code>NA</code> of class <code>character</code>)</li>
|
||||
<li>The <code><a href="../reference/proportion.html">proportion_df()</a></code>, <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/proportion.html">rsi_df()</a></code> functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages</li>
|
||||
|
|
@ -327,7 +328,7 @@
|
|||
<li>The documentation of the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely rewritten.</li>
|
||||
</ul></li>
|
||||
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code>filter_betalactams()</code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
|
||||
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
|
|
@ -362,8 +363,8 @@
|
|||
<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code> on an RSI class</li>
|
||||
<li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
|
||||
<li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
|
||||
<li>Fix for using <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
|
||||
<li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> usage for MIC values to also include 25th and 75th percentiles</li>
|
||||
<li>Fix for using <code>skimr::skim()</code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
|
||||
<li>Updated <code>skimr::skim()</code> usage for MIC values to also include 25th and 75th percentiles</li>
|
||||
<li>Fix for plotting missing MIC/disk diffusion values</li>
|
||||
<li>Updated join functions to always use <code>dplyr</code> join functions if the <code>dplyr</code> package is installed - now also preserving grouped variables</li>
|
||||
<li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
|
||||
|
|
@ -410,7 +411,7 @@
|
|||
<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
|
||||
<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||||
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
|
|
@ -461,7 +462,7 @@
|
|||
<ul><li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
|
||||
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
|
||||
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
|
||||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
|
||||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
|
||||
</ul></li>
|
||||
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
|
||||
<li>
|
||||
|
|
@ -756,7 +757,7 @@
|
|||
<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
|
||||
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
|
||||
<p>Negative effects of this change are:</p>
|
||||
<ul><li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
|
||||
<ul><li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>.</li>
|
||||
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
||||
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
||||
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
||||
|
|
@ -1019,7 +1020,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
|
||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||
</li>
|
||||
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
|
|
@ -1248,7 +1249,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
|
||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
||||
</li>
|
||||
<li>Frequency tables (<code>freq()</code>):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>):
|
||||
<ul><li><p>speed improvement for microbial IDs</p></li>
|
||||
<li><p>fixed factor level names for R Markdown</p></li>
|
||||
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
|
||||
|
|
@ -1257,12 +1258,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul></li>
|
||||
|
|
@ -1271,7 +1272,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||
</li>
|
||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
||||
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
|
||||
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> for when all values are <code>NA</code>
|
||||
</li>
|
||||
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
||||
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
||||
|
|
@ -1474,7 +1475,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li>Now accepts high and low resistance: <code>"HIGH S"</code> will return <code>S</code>
|
||||
</li>
|
||||
</ul></li>
|
||||
<li>Frequency tables (<code>freq()</code> function):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function):
|
||||
<ul><li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||
|
|
@ -1483,15 +1484,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<span class="co"># OLD WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
|
|
@ -1560,21 +1561,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
|
||||
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
|
||||
<li>
|
||||
<p>Frequency tables - <code>freq()</code>:</p>
|
||||
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>:</p>
|
||||
<ul><li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html" class="external-link">hms::is.hms</a></code></p></li>
|
||||
|
|
@ -1591,7 +1592,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
|
||||
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
|
||||
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">top_freq()</a></code></p></li>
|
||||
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
|
||||
<li>
|
||||
<p>AI improvements for <code>as.mo</code>:</p>
|
||||
|
|
@ -1740,13 +1741,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||
<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level5">
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
pandoc: 2.14.0.3
|
||||
pkgdown: 2.0.0
|
||||
pandoc: 2.9.2.1
|
||||
pkgdown: 2.0.2
|
||||
pkgdown_sha: ~
|
||||
articles:
|
||||
AMR: AMR.html
|
||||
|
|
@ -12,7 +12,7 @@ articles:
|
|||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-12-23T17:53Z
|
||||
last_built: 2022-03-12T18:42Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,6 @@
|
|||
<p>Welcome to the <code>AMR</code> package.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,NULL</div>
|
||||
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
|
|
@ -226,7 +225,7 @@ The Netherlands
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">WHONET</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">WHONET</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -217,7 +219,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -275,13 +275,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -344,13 +344,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -226,13 +226,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -250,13 +250,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -430,13 +430,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -280,13 +280,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -239,13 +239,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -273,13 +273,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -377,13 +377,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -334,7 +334,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
<span class="co"># \donttest{</span>
|
||||
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://docs.ropensci.org/skimr/" class="external-link">"skimr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
|
||||
<span class="co"># class <rsi> supported in skim() too:</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skim</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="fu">skim</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="op">}</span>
|
||||
<span class="co"># }</span>
|
||||
<span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span>
|
||||
|
|
@ -423,13 +423,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -257,13 +257,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -216,13 +216,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -265,13 +265,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -301,13 +301,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href="eucast_rules.html">eucast_dosage()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dosage</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dosage</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -204,7 +206,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -334,13 +334,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -201,7 +203,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates_unclean</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates_unclean</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -196,7 +198,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -371,13 +371,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -278,13 +278,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -304,13 +304,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -395,13 +395,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -243,13 +243,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -157,10 +157,7 @@
|
|||
|
||||
<table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
|
||||
<h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of
|
||||
microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach
|
||||
this package how to translate your own codes to valid microorganism
|
||||
codes.</p>
|
||||
<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><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">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
|
||||
|
|
@ -176,9 +173,7 @@ codes.</p>
|
|||
<td><p>User-Defined Reference Data Set for Microorganisms</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any
|
||||
input or to clean your input. You can even retrieve drug names and doses
|
||||
from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
|
||||
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
|
||||
|
|
@ -198,13 +193,7 @@ from clinical text records, using <code><a href="../reference/ab_from_text.html"
|
|||
<td><p>Get ATC Properties from WHOCC Website</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can
|
||||
transform your raw input to valid MIC or disk diffusion values. Use
|
||||
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”,
|
||||
“I” and “S”, or to interpret MIC or disk diffusion values as R/SI based
|
||||
on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend
|
||||
antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||||
rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
|
||||
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_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>
|
||||
|
|
@ -228,14 +217,7 @@ rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a>
|
|||
<td><p>Define Custom EUCAST Rules</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>Use these function for the analysis part. You can use
|
||||
<code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any
|
||||
antibiotic column. Be sure to first select the isolates that are
|
||||
appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or
|
||||
<code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain
|
||||
resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>,
|
||||
<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant
|
||||
microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
|
||||
<p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
|
||||
|
|
@ -287,9 +269,7 @@ microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).
|
|||
<td><p>Guess Antibiotic Column</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to
|
||||
read our <a href="./../articles/index.html">How To’s</a> for more
|
||||
information about how to work with functions in this package.</p>
|
||||
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||||
|
|
@ -353,9 +333,7 @@ information about how to work with functions in this package.</p>
|
|||
<td><p>Data Set with 500 Isolates - WHONET Example</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may
|
||||
also be suitable for your analysis. Especially the ‘like’ function can
|
||||
be useful: <code>if (x %like% y) {...}</code>.</p>
|
||||
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
|
||||
|
|
@ -403,8 +381,7 @@ be useful: <code>if (x %like% y) {...}</code>.</p>
|
|||
<td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were
|
||||
added to this package for convenience.</p>
|
||||
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="g.test.html">g.test()</a></code> </p>
|
||||
|
|
@ -420,9 +397,7 @@ added to this package for convenience.</p>
|
|||
<td><p>Skewness of the Sample</p></td>
|
||||
</tr></tbody><tbody><tr><th colspan="2">
|
||||
<h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
|
||||
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but
|
||||
show a warning with every use and will be removed in a future
|
||||
version.</p>
|
||||
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
|
||||
</th>
|
||||
</tr></tbody><tbody><tr><td>
|
||||
<p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p>
|
||||
|
|
@ -437,13 +412,11 @@ version.</p>
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">intrinsic_resistant</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">intrinsic_resistant</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -212,7 +214,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -221,13 +221,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -242,13 +242,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -308,13 +308,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -211,13 +211,11 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -260,13 +260,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -352,13 +352,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -231,13 +231,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -433,13 +433,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -267,13 +267,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -266,13 +266,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -332,13 +332,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -381,13 +381,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -232,13 +232,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -161,7 +161,9 @@
|
|||
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div></div>
|
||||
<div id="ref-usage">
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div>
|
||||
</div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
|
@ -210,7 +212,7 @@
|
|||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
|
|
@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
|
|
|||
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Loading…
Reference in New Issue