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prerelease 1.8.1

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Merge branch 'development' of https://github.com/msberends/AMR into development

# Conflicts:
#	docs/articles/AMR.html
#	docs/articles/AMR_files/figure-html/disk_plots-1.png
#	docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
#	docs/articles/AMR_files/figure-html/mic_plots-1.png
#	docs/articles/AMR_files/figure-html/mic_plots-2.png
#	docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
#	docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
#	docs/articles/AMR_files/figure-html/plot 1-1.png
#	docs/articles/AMR_files/figure-html/plot 3-1.png
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#	docs/articles/AMR_files/figure-html/plot 5-1.png
#	docs/articles/EUCAST.html
#	docs/articles/MDR.html
#	docs/articles/PCA.html
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#	docs/articles/benchmarks.html
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#	docs/articles/datasets.html
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#	docs/articles/welcome_to_AMR.html
#	docs/news/index.html
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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-03-14 16:37:37 +01:00
parent 1b0983e382 8c9feea087
commit 45e9546538
73 changed files with 1231 additions and 1020 deletions
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69
docs/articles/MDR.html
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@ -44,7 +44,11 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span>
</div>
@ -185,7 +189,7 @@
</header><div class="row">
</header><script src="MDR_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 determine multi-drug resistance
@ -343,6 +347,7 @@ on this data set, we get:</p>
<span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
<span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
<<<<<<< HEAD
<p>Only results with ‘R’ are considered as resistance. Use
<code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
<p>Determining multidrug-resistant organisms (MDRO), according to:
@ -352,6 +357,10 @@ 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>
=======
<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<p>(16 isolates had no test results)</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
@ -422,6 +431,7 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<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>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<<<<<<< HEAD
<span class="co"># 1 R S S I S I</span>
<span class="co"># 2 R S S S R I</span>
<span class="co"># 3 S S I I S S</span>
@ -437,6 +447,22 @@ names or codes, this would have worked exactly the same way:</p>
<span class="co"># 6 I</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
=======
<span class="co"># 1 I R I R I I</span>
<span class="co"># 2 I R I I I I</span>
<span class="co"># 3 S I I R S S</span>
<span class="co"># 4 R I R I R I</span>
<span class="co"># 5 S I S S R S</span>
<span class="co"># 6 S S I I I S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 I</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -462,8 +488,12 @@ use:</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000<br>
<<<<<<< HEAD
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt;
Multi-drug-resistant &lt;…<br>
=======
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
Available: 5,000 (100%, NA: 0 = 0%)<br>
Unique: 5</p>
<table style="width:100%;" class="table">
@ -487,40 +517,73 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<<<<<<< HEAD
<td align="right">3175</td>
<td align="right">63.50%</td>
<td align="right">3175</td>
<td align="right">63.50%</td>
=======
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<<<<<<< HEAD
<td align="right">1057</td>
<td align="right">21.14%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
=======
<td align="right">969</td>
<td align="right">19.38%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<<<<<<< HEAD
<td align="right">431</td>
<td align="right">8.62%</td>
<td align="right">4663</td>
<td align="right">93.26%</td>
=======
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<<<<<<< HEAD
<td align="right">236</td>
<td align="right">4.72%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
=======
<td align="right">263</td>
<td align="right">5.26%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<<<<<<< HEAD
<td align="right">101</td>
<td align="right">2.02%</td>
=======
<td align="right">100</td>
<td align="right">2.00%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@ -545,8 +608,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown">
<p></p>
<<<<<<< HEAD
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div>
</footer>