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(v1.3.0.9015) as.mo() speedup for valid taxonomic names

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dr. M.S. (Matthijs) Berends
2020-09-03 20:59:21 +02:00
parent c4b87fe241
commit 68e9cb78e9
104 changed files with 542 additions and 529 deletions
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docs/articles/MDR.html
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@ -39,7 +39,7 @@
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@ -320,19 +320,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I S S S S R</span>
<span class="co"># 2 S S S R R I</span>
<span class="co"># 3 R S S R S I</span>
<span class="co"># 4 R S S R S S</span>
<span class="co"># 5 S R I R I R</span>
<span class="co"># 6 R R S R R R</span>
<span class="co"># 1 S R S S R S</span>
<span class="co"># 2 S R R S R S</span>
<span class="co"># 3 S R R S S R</span>
<span class="co"># 4 R R S S S R</span>
<span class="co"># 5 I S I S S S</span>
<span class="co"># 6 S S R R S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span>
<span class="co"># 1 R</span>
<span class="co"># 2 I</span>
<span class="co"># 3 S</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
@ -368,40 +368,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">698</td>
<td align="right">13.96%</td>
<td align="right">3931</td>
<td align="right">78.62%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">614</td>
<td align="right">12.28%</td>
<td align="right">3911</td>
<td align="right">78.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">556</td>
<td align="right">11.12%</td>
<td align="right">4487</td>
<td align="right">89.74%</td>
<td align="left">Negative</td>
<td align="right">603</td>
<td align="right">12.06%</td>
<td align="right">4514</td>
<td align="right">90.28%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">300</td>
<td align="right">6.00%</td>
<td align="right">4787</td>
<td align="right">95.74%</td>
<td align="right">278</td>
<td align="right">5.56%</td>
<td align="right">4792</td>
<td align="right">95.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">213</td>
<td align="right">4.26%</td>
<td align="right">208</td>
<td align="right">4.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>