P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:01:50 +02:00
Code Releases Activity

(v0.7.1.9027) tibble printing

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-07 15:37:39 +02:00
parent 14c47da656
commit 90c874025a
42 changed files with 946 additions and 602 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
docs/articles/MDR.html
View File

@ -40,7 +40,7 @@
</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="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">06 August 2019</h4>
<h4 class="date">07 August 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -228,16 +228,16 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R R S R S S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R R S R S S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R S R S S R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 R I S R R R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 I S S R I S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R R R S I S</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R R S S I S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S S S R R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S S S S R R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S S R S R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 S R R R R R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 S S R S S I</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 I</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
@ -272,39 +272,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
<td align="right">3271</td>
<td align="right">65.4%</td>
<td align="right">3271</td>
<td align="right">65.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">627</td>
<td align="right">12.5%</td>
<td align="right">3891</td>
<td align="right">77.8%</td>
<td align="right">643</td>
<td align="right">12.9%</td>
<td align="right">3914</td>
<td align="right">78.3%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">607</td>
<td align="right">12.1%</td>
<td align="right">4498</td>
<td align="right">90.0%</td>
<td align="right">582</td>
<td align="right">11.6%</td>
<td align="right">4496</td>
<td align="right">89.9%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">288</td>
<td align="right">5.8%</td>
<td align="right">4786</td>
<td align="right">287</td>
<td align="right">5.7%</td>
<td align="right">4783</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">214</td>
<td align="right">217</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>