Commit 6eef17ba authored by Jakob Wirbel's avatar Jakob Wirbel

re-build website with pkgdown (without custom url).

parent b0f99e50
......@@ -11,7 +11,7 @@
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="Holdout Testing with SIAMCAT">
<meta property="og:description" content="">
<meta property="og:image" content="http://siamcat.embl.de/logo.png">
<meta property="og:image" content="/logo.png">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
......@@ -145,13 +145,13 @@ 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 0.023 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.015 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 0.073 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>,
......@@ -176,7 +176,7 @@ 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 0.044 s</code></pre>
<pre><code>## + finished validate.data in 0.032 s</code></pre>
</div>
<div id="model-building-on-the-french-dataset" class="section level1">
<h1 class="hasAnchor">
......@@ -196,7 +196,7 @@ 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 0.004 s</code></pre>
<pre><code>## + finished filter.features in 0.003 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>,
......@@ -207,7 +207,7 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## +++ performing de novo normalization using the log.std method</code></pre>
<pre><code>## + feature sparsity before normalization: 46.05%</code></pre>
<pre><code>## +++ feature sparsity after normalization: 0 %</code></pre>
<pre><code>## + finished normalize.features in 0.005 s</code></pre>
<pre><code>## + finished normalize.features in 0.004 s</code></pre>
</div>
<div id="model-training" class="section level2">
<h2 class="hasAnchor">
......@@ -251,7 +251,7 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## + performing frozen log.std normalization using the supplied parameters</code></pre>
<pre><code>## + feature sparsity before normalization: 49.77%</code></pre>
<pre><code>## + feature sparsity after normalization: 0%</code></pre>
<pre><code>## + finished normalize.features in 0.007 s</code></pre>
<pre><code>## + finished normalize.features in 0.005 s</code></pre>
</div>
<div id="holdout-predictions" class="section level2">
<h2 class="hasAnchor">
......
......@@ -11,7 +11,7 @@
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="SIAMCAT input files formats">
<meta property="og:description" content="">
<meta property="og:image" content="http://siamcat.embl.de/logo.png">
<meta property="og:image" content="/logo.png">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
......@@ -412,7 +412,7 @@ feat &lt;-<span class="st"> </span>meta.and.features<span class="op">$</span>fea
## cancer
## Label used as control:
## healthy</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.017 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.015 s</code></pre>
</div>
<div id="metagenomeseq-format-files" class="section level2">
<h2 class="hasAnchor">
......@@ -454,7 +454,7 @@ label &lt;-<span class="st"> </span><span class="kw"><a href="../reference/creat
## Freshwater,Freshwater (creek),Ocean
## Label used as control:
## rest</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.004 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.003 s</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># run the constructor function</span>
siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/siamcat.html">siamcat</a></span>(<span class="dt">phyloseq=</span>GlobalPatterns, <span class="dt">label=</span>label)</code></pre></div>
<pre><code>## + starting validate.data</code></pre>
......@@ -464,7 +464,7 @@ 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 0.546 s</code></pre>
<pre><code>## + finished validate.data in 0.439 s</code></pre>
</div>
</div>
<div id="creating-a-siamcat-class-object" class="section level1">
......
......@@ -11,7 +11,7 @@
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes">
<meta property="og:description" content="">
<meta property="og:image" content="http://siamcat.embl.de/logo.png">
<meta property="og:image" content="/logo.png">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
......@@ -162,7 +162,7 @@
<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 0.062 s</code></pre>
<pre><code>## + finished validate.data in 0.058 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
......@@ -247,13 +247,13 @@ 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 0.07965817 0.1120344
## CCIS15794887ST-4-0 0.14819959 0.1396626
## CCIS74726977ST-3-0 0.39648685 0.3248774
## CCIS16561622ST-4-0 0.14219439 0.4685665
## CCIS79210440ST-3-0 0.22730698 0.1913344
## CCIS82507866ST-3-0 0.28556249 0.3349436</code></pre>
<pre><code>## CV_rep1 CV_rep2
## CCIS27304052ST-3-0 0.19880497 0.09535739
## CCIS15794887ST-4-0 0.25670422 0.16473066
## CCIS74726977ST-3-0 0.59187395 0.63774235
## CCIS16561622ST-4-0 0.54217795 0.09439314
## CCIS79210440ST-3-0 0.28578571 0.23673264
## CCIS82507866ST-3-0 0.08502265 0.07268986</code></pre>
</div>
</div>
<div id="model-evaluation-and-interpretation" class="section level1">
......
......@@ -32,7 +32,7 @@
<meta property="og:title" content="Articles" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -32,7 +32,7 @@
<meta property="og:title" content="Citation and Authors" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -24,7 +24,7 @@
including tools for evaluation and interpretation of these models (such as
cross validation, parameter selection, ROC analysis and diagnostic
model plots).">
<meta property="og:image" content="http://siamcat.embl.de/logo.png">
<meta property="og:image" content="/logo.png">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
......@@ -277,4 +277,3 @@ eLife, (<strong>2019</strong>) 8:e42693</p>
</body>
</html>
......@@ -5,7 +5,4 @@ articles:
SIAMCAT_holdout: SIAMCAT_holdout.html
SIAMCAT_read-in: SIAMCAT_read-in.html
SIAMCAT_vignette: SIAMCAT_vignette.html
urls:
reference: http://siamcat.embl.de/reference
article: http://siamcat.embl.de/articles
......@@ -48,7 +48,7 @@ Pipeline for Statistical Inference of Associations between
cross validation, parameter selection, ROC analysis and diagnostic
model plots)." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="This function is used internally by many accessors." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="This function adds metadata to the feature matrix to be later
used as predictors" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new assocications object to x" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -37,7 +37,7 @@ SIAMCAT object — data_split&lt;-" />
<meta property="og:description" content="Assign a new list containing a cross-validation split to a
SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new list with evaluation data to a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new filt_feat object to x" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new label object to a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new sam_data object to x" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new list containing trained models to a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -37,7 +37,7 @@ features to a SIAMCAT object — norm_feat&lt;-" />
<meta property="og:description" content="Assign a new list containing normalziation parameters and normalized
features to a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new otu_table object to x orig_feat slot" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new phyloseq object to x" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Assign a new matrix with predictions to a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -37,7 +37,7 @@ a SIAMCAT object — assoc_param" />
<meta property="og:description" content="Function to retrieve the list of parameters for
association testing" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Function to retrieve the results of association testing" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="This function computes different measures of association between
features and the label and visualizes the results" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="Checks potential confounders in the metadata and produces
some visualizations" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -36,7 +36,7 @@
data into num.folds training and test folds for
num.resample times." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="This function creates a label object from metadata
or an atomic vector" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......@@ -224,7 +224,7 @@ 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 0.002 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 0.001 s</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve the data split stored in the
data_split slot within a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve the evaluation metrics from a SIAMCAT
object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -42,7 +42,7 @@ as metric. Predictions can be supplied either for a single case or as
Prediction results are usually produced with the function
make.predictions." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -36,7 +36,7 @@
et al. MSB 2014 (see http://msb.embopress.org/content/10/11/766),
containing 141 samples and 1754 bacterial species (features)." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -37,7 +37,7 @@ object — feature_type" />
<meta property="og:description" content="Function to retrieve information on which type of features the
models were trained" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -34,7 +34,7 @@
<meta property="og:description" content="Function to extract the feature weights from a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
......
......@@ -37,7 +37,7 @@ a SIAMCAT object — filt_feat" />
<meta property="og:description" content="Function to retrieve the information stored in the
filt_feat slot within a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@ SIAMCAT object — filt_params" />
<meta property="og:description" content="Function to retrieve the list of parameters for feature
filtering" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -36,7 +36,7 @@
can be filtered based on abundance, prevalence, or on variance.
Additionally, unmapped reads may be removed." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="This functions filters the label in a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="Show the component objects classes and slot names." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve the filtered features from a SIAMCAT
object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve the normalized features from a SIAMCAT
object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve the original features from a SIAMCAT
object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -32,7 +32,7 @@
<meta property="og:title" content="Function reference" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="Retrieve the label from a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -36,7 +36,7 @@
a model trained by train.model and performs predictions on
a given test-set." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="Retrieve the metadata from a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -36,7 +36,7 @@
al. MSB 2014 (see http://msb.embopress.org/content/10/11/766),
containing 6 metadata variables variables (e.g. Age or BMI) for 141 samples." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@
Precision-recall (PR)-curves for the different cross-validation
repetitions." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -41,7 +41,7 @@ the distribution of metadata across samples, and
the proportion of model weights shown.
" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@ a SIAMCAT object — model_list" />
<meta property="og:description" content="Function to retrieve the information stored in the
model_list slot within a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -35,7 +35,7 @@
<meta property="og:description" content="Function to retrieve information on which type of machine
learning method was used for model training" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="Function to retrieve the list of trained models" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@ a SIAMCAT object — norm_feat" />
<meta property="og:description" content="Function to retrieve the information stored in the
norm_feat slot within a SIAMCAT object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@ SIAMCAT object — norm_params" />
<meta property="og:description" content="Function to retrieve the list of parameters for feature
normalization" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -35,7 +35,7 @@
<meta property="og:description" content="This function performs feature normalization according to user-
specified parameters." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -37,7 +37,7 @@ the phyloseq slot in a siamcat object — orig_feat" />
<meta property="og:description" content="Retrieve a otu_table-class object from otu_table slot in
the phyloseq slot in a siamcat object" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="This function parses the header of a label file" />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
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......@@ -34,7 +34,7 @@
<meta property="og:description" content="Retrieve a phyloseq-class object from object." />
<meta property="og:image" content="http://siamcat.embl.de/logo.png" />
<meta property="og:image" content="/logo.png" />