P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:47:54 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9135@8dcf101

Browse Source
This commit is contained in:
github-actions
2023-02-18 12:17:35 +00:00
parent 2183549fea
commit cdada2f940
101 changed files with 719 additions and 724 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
articles/SPSS.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 February 2023</h4>
<h4 data-toc-skip class="date">18 February 2023</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="d-none name"><code>SPSS.Rmd</code></div>
@ -324,15 +324,15 @@ would be of any better use than R.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># not all values are valid MIC values:</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.125</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 0.125</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] &lt;NA&gt;</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] &lt;NA&gt;</span></span>
<span></span>
<span><span class="co"># the Gram stain is available for all bacteria:</span></span>
<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>
<span><span class="co"># [1] "Gram-negative"</span></span>
<span><span class="co">#&gt; [1] "Gram-negative"</span></span>
<span></span>
<span><span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span></span>
<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" class="external-link">data.frame</a></span><span class="op">(</span></span>
@ -341,22 +341,22 @@ would be of any better use than R.</p>
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span>
<span><span class="va">klebsiella_test</span> <span class="co"># (our original data)</span></span>
<span><span class="co"># mo amox</span></span>
<span><span class="co"># 1 klebsiella S</span></span>
<span><span class="co">#&gt; mo amox</span></span>
<span><span class="co">#&gt; 1 klebsiella S</span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">klebsiella_test</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="co"># (the edited data by EUCAST rules)</span></span>
<span><span class="co"># mo amox</span></span>
<span><span class="co"># 1 klebsiella R</span></span>
<span><span class="co">#&gt; mo amox</span></span>
<span><span class="co">#&gt; 1 klebsiella R</span></span>
<span></span>
<span><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "Flucloxacillin"</span></span>
<span><span class="co">#&gt; [1] "Flucloxacillin"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "culpen" "floxacillin" "floxacillin sodium" </span></span>
<span><span class="co"># [4] "floxapen" "floxapen sodium salt" "fluclox" </span></span>
<span><span class="co"># [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span></span>
<span><span class="co"># [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex"</span></span>
<span><span class="co">#&gt; [1] "culpen" "floxacillin" "floxacillin sodium" </span></span>
<span><span class="co">#&gt; [4] "floxapen" "floxapen sodium salt" "fluclox" </span></span>
<span><span class="co">#&gt; [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span></span>
<span><span class="co">#&gt; [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex"</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span></span>
<span><span class="co"># [1] "J01CF05"</span></span></code></pre></div>
<span><span class="co">#&gt; [1] "J01CF05"</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="import-data-from-spsssasstata">Import data from SPSS/SAS/Stata<a class="anchor" aria-label="anchor" href="#import-data-from-spsssasstata"></a>