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(v1.5.0.9013) updated tibble printing colours

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dr. M.S. (Matthijs) Berends
2021-01-28 16:09:30 +01:00
parent 331c1f6508
commit 20d638c193
39 changed files with 162 additions and 108 deletions
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58
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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9013</span>
</span>
</div>
@ -339,19 +339,19 @@ Unique: 2</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">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>
<span class="co"># 1 I R I R I I</span>
<span class="co"># 2 R R I S R I</span>
<span class="co"># 3 I S S I S I</span>
<span class="co"># 4 I I R S R I</span>
<span class="co"># 5 I R I S S I</span>
<span class="co"># 6 S I I I R R</span>
<span class="co"># 1 R I I R R R</span>
<span class="co"># 2 R S I S R S</span>
<span class="co"># 3 R R S S R I</span>
<span class="co"># 4 S R R S S R</span>
<span class="co"># 5 I R R R R S</span>
<span class="co"># 6 I I I R S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 I</span></code></pre></div>
<span class="co"># 4 S</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>
<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>
@ -382,40 +382,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3228</td>
<td align="right">64.56%</td>
<td align="right">3228</td>
<td align="right">64.56%</td>
<td align="right">3163</td>
<td align="right">63.26%</td>
<td align="right">3163</td>
<td align="right">63.26%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1017</td>
<td align="right">20.34%</td>
<td align="right">4245</td>
<td align="right">84.90%</td>
<td align="right">1009</td>
<td align="right">20.18%</td>
<td align="right">4172</td>
<td align="right">83.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">421</td>
<td align="right">8.42%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
<td align="right">466</td>
<td align="right">9.32%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">231</td>
<td align="right">4.62%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

8
docs/articles/SPSS.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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9013</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 January 2021</h4>
<h4 class="date">28 January 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -256,11 +256,11 @@
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] &lt;NA&gt;</span>
<span class="co"># the Gram stain is avaiable for all bacteria:</span>
<span class="co"># the Gram stain is available for all bacteria:</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># [1] "Gram-negative"</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span>
<span class="va">klebsiella_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>,
amox <span class="op">=</span> <span class="st">"S"</span>,
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9013</span>
</span>
</div>