Commit 4551f144 authored by Jakob Wirbel's avatar Jakob Wirbel

add privacy statement in the footer of the website.

parent 9bc6a616
......@@ -156,13 +156,13 @@ siamcat.fr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
## CRC
## Label used as control:
## CTR</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.015 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.016 s</code></pre>
<pre><code>## + starting validate.data</code></pre>
<pre><code>## +++ checking overlap between labels and features</code></pre>
<pre><code>## + Keeping labels of 141 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.039 s</code></pre>
<pre><code>## + finished validate.data in 0.041 s</code></pre>
<p>We can load the data from the Chinese study in a similar way and also create a <code>SIAMCAT</code> object for the holdout dataset.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># features</span>
feat.cn &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/read.table">read.table</a></span>(fn.feat.cn, <span class="dt">sep=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>, <span class="dt">quote=</span><span class="st">""</span>,
......@@ -187,7 +187,7 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## + Keeping labels of 128 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.031 s</code></pre>
<pre><code>## + finished validate.data in 0.034 s</code></pre>
</div>
<div id="model-building-on-the-french-dataset" class="section level1">
<h1 class="hasAnchor">
......@@ -207,7 +207,7 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## +++ before filtering, the data have 1754 features</code></pre>
<pre><code>## +++ removed 1 features corresponding to UNMAPPED reads</code></pre>
<pre><code>## +++ removed 1538 features whose values did not exceed 0.001 in any sample (retaining 215)</code></pre>
<pre><code>## + finished filter.features in 0.003 s</code></pre>
<pre><code>## + finished filter.features in 0.007 s</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">siamcat.fr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/normalize.features.html">normalize.features</a></span>(
siamcat.fr,
<span class="dt">norm.method =</span> <span class="st">"log.std"</span>,
......@@ -386,8 +386,11 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -475,7 +475,7 @@ siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/sia
<pre><code>## Data set has only 8 training examples of class Case .
## Note that a dataset this small/skewed is not necessarily suitable for analysis in this pipeline.</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.433 s</code></pre>
<pre><code>## + finished validate.data in 0.443 s</code></pre>
</div>
</div>
<div id="creating-a-siamcat-class-object" class="section level1">
......@@ -644,8 +644,11 @@ tax_tab &lt;-<span class="st"> </span><span class="kw">tax_table</span>(phyloseq
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -163,7 +163,7 @@
## CRC
## Label used as control:
## CTR</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.001 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.002 s</code></pre>
<p>Now we have all the ingredients to create a <code>SIAMCAT</code> object. Please have a look at the <a href="SIAMCAT_read-in.html">vignette about input formats</a> for more information about supported formats and other ways to create a <code>SIAMCAT</code> object.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/siamcat.html">siamcat</a></span>(<span class="dt">feat=</span>feat.crc.zeller,
<span class="dt">label=</span>label.crc.zeller,
......@@ -173,7 +173,7 @@
<pre><code>## + Keeping labels of 141 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.057 s</code></pre>
<pre><code>## + finished validate.data in 0.055 s</code></pre>
<p>A few information about the <code>siamcat</code> object can be accessed with the <code>show</code> function from <code>phyloseq</code> (<code>SIAMCAT</code> builds on the <code>phyloseq</code> data structure):</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">show</span>(siamcat)</code></pre></div>
<pre><code>## siamcat-class object
......@@ -258,13 +258,13 @@ models[[<span class="dv">1</span>]]</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/make.predictions.html">make.predictions</a></span>(siamcat)
pred_matrix &lt;-<span class="st"> </span><span class="kw"><a href="../reference/pred_matrix-methods.html">pred_matrix</a></span>(siamcat)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(pred_matrix)</code></pre></div>
<pre><code>## CV_rep1 CV_rep2
## CCIS27304052ST-3-0 0.05627524 0.1227390
## CCIS15794887ST-4-0 0.06400252 0.0941945
## CCIS74726977ST-3-0 0.41996493 0.2777645
## CCIS16561622ST-4-0 0.34675575 0.2208130
## CCIS79210440ST-3-0 0.44411220 0.1147398
## CCIS82507866ST-3-0 0.07560513 0.0656949</code></pre>
<pre><code>## CV_rep1 CV_rep2
## CCIS27304052ST-3-0 0.06397577 0.11698094
## CCIS15794887ST-4-0 0.17410869 0.15642467
## CCIS74726977ST-3-0 0.26392649 0.28947756
## CCIS16561622ST-4-0 0.23262730 0.41677000
## CCIS79210440ST-3-0 0.35229355 0.21137621
## CCIS82507866ST-3-0 0.06326147 0.04334376</code></pre>
</div>
</div>
<div id="model-evaluation-and-interpretation" class="section level1">
......@@ -395,8 +395,11 @@ pred_matrix &lt;-<span class="st"> </span><span class="kw"><a href="../reference
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -133,8 +133,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -171,8 +171,11 @@ doi: <a href="http://doi.org/10.18129/B9.bioc.SIAMCAT">10.18129/B9.bioc.SIAMCAT<
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -285,8 +285,11 @@ Nature Medicine, (<strong>2019</strong>) [Epub ahead of print]</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -194,8 +194,11 @@ extraction toolkits are crucially needed!</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -312,8 +312,11 @@ can be either 0 (no output) or 1 (print message)</p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -214,8 +214,11 @@ numerically before you start the SIAMCAT workflow.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -172,8 +172,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -175,8 +175,11 @@ SIAMCAT object</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -172,8 +172,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -175,8 +175,11 @@ features to a SIAMCAT object</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -170,8 +170,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -186,8 +186,11 @@ testing. See <a href='check.associations.html'>check.associations</a> for more d
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -207,8 +207,11 @@ procedure as dataframe. See <a href='check.associations.html'>check.associations
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -282,8 +282,11 @@ defaults to <code>1</code></p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -200,8 +200,11 @@ defaults to <code>1</code></p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -234,8 +234,11 @@ defaults to <code>1</code></p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -216,7 +216,7 @@ contains the label information.</p>
<span class='no'>label</span> <span class='kw'>&lt;-</span> <span class='fu'>create.label</span>(<span class='kw'>label</span><span class='kw'>=</span><span class='st'>'Group'</span>, <span class='kw'>case</span><span class='kw'>=</span><span class='st'>'CRC'</span>, <span class='kw'>meta</span><span class='kw'>=</span><span class='no'>meta.crc.zeller</span>)</div><div class='output co'>#&gt; <span class='message'>Label used as case:</span>
#&gt; <span class='message'> CRC</span>
#&gt; <span class='message'>Label used as control:</span>
#&gt; <span class='message'> CTR</span></div><div class='output co'>#&gt; <span class='message'>+ finished create.label.from.metadata in 0.001 s</span></div></pre>
#&gt; <span class='message'> CTR</span></div><div class='output co'>#&gt; <span class='message'>+ finished create.label.from.metadata in 0.002 s</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
......@@ -238,8 +238,11 @@ contains the label information.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -182,8 +182,11 @@ split. See <a href='create.data.split.html'>create.data.split</a> for more detai
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -184,8 +184,11 @@ evaluation data.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -222,8 +222,11 @@ defaults to <code>1</code></p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -151,8 +151,11 @@ containing 141 samples and 1754 bacterial species (features).</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -185,8 +185,11 @@ the models were trained.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -215,8 +215,11 @@ selected (i.e. non-zero)</p></li>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -191,8 +191,11 @@ in the <code>filt_feat</code> slot of a SIAMCAT object. This list contains:</p><
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -185,8 +185,11 @@ See <a href='filter.features.html'>filter.features</a> for more details.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -233,8 +233,11 @@ defaults to <code>1</code></p></td>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -188,8 +188,11 @@ filtering the label.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -148,8 +148,11 @@
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -181,8 +181,11 @@ See <a href='filter.features.html'>filter.features</a> for more details.</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -181,8 +181,11 @@ See <a href='normalize.features.html'>normalize.features</a> for more details.</
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>
</div>
</footer>
</div>
......
......@@ -179,8 +179,11 @@ object</p>
<p>Developed by Konrad Zych, Jakob Wirbel, Georg Zeller.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<div class="privacy">
<p><strong>Privacy:</strong> Usage of this site follows
<a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL’s Privacy Policy</a><br/>
In accordance with that policy, we use Matomo to collect anonymised data on visits to, downloads from, and searches of this site.
Contact <a href="mailto:zeller@embl.de">Georg Zeller</a> for details.</p>