diff --git a/README.md b/README.md
index b3dd654..7f5e44b 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@ PhylogeneticEM
 Implementation of the EM algorithm for the detection of shifts in a phylogeny.
 
 ## Installation
-Stable version (1.0.0) on the [CRAN](https://cran.rstudio.com/web/packages/PhylogeneticEM/).
+Stable version on the [CRAN](https://cran.rstudio.com/web/packages/PhylogeneticEM/).
 
 To get the latest (and possibly unstable) version, you can use the [`devtools`](https://github.com/hadley/devtools) package:
 ```R
diff --git a/docs/articles/index.html b/docs/articles/index.html
index d23c2fa..8b70191 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -74,7 +74,7 @@
       </header>
 
       <div class="page-header">
-  <h1>Vignette reference <small>version&nbsp;1.0.0.9000</small></h1>
+  <h1>Articles <small>version&nbsp;1.0.1</small></h1>
 </div>
 
 <div class="row">
diff --git a/docs/articles/tutorial.html b/docs/articles/tutorial.html
index eceb01f..1bff146 100644
--- a/docs/articles/tutorial.html
+++ b/docs/articles/tutorial.html
@@ -9,7 +9,7 @@
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 <!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -57,7 +57,7 @@
       <h1>An Introduction to the PhylogeneticEM Package</h1>
                         <h4 class="author">Paul Bastide</h4>
             
-            <h4 class="date">2017-04-10</h4>
+            <h4 class="date">2017-05-01</h4>
           </div>
 
     
diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-2-1.png
index e5b7eab..e05f429 100644
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diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-4-1.png
index 1b7ae74..6d90060 100644
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index 1b7ae74..6d90060 100644
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diff --git a/docs/authors.html b/docs/authors.html
index 0a1d944..ac0e5fc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -25,7 +25,7 @@
 <script src="pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
diff --git a/docs/index.html b/docs/index.html
index 753ccdb..1b7b3e0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,7 +9,7 @@
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 <!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -97,7 +97,6 @@ <h2>Developers</h2>
 <li>Paul Bastide <br><small class="roles"> Author, maintainer </small> </li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
-<div>
 <h2>Dev status</h2>
 <ul class="list-unstyled">
 <li><a href="https://travis-ci.org/pbastide/PhylogeneticEM"><img src="https://travis-ci.org/pbastide/PhylogeneticEM.svg?branch=master" alt="Travis-CI Build Status"></a></li>
@@ -106,7 +105,6 @@ <h2>Dev status</h2>
 <li><a href="https://CRAN.R-project.org/package=PhylogeneticEM"><img src="https://www.r-pkg.org/badges/version/PhylogeneticEM" alt="CRAN_Status_Badge"></a></li>
 </ul>
 </div>
-</div>
 </div>
 
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 0dc8f56..320c170 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -81,16 +81,21 @@ <h1>Change log <small>All releases</small></h1>
     </div>
 
     <div class="contents">
-    <div id="phylogeneticem-1-0-0-900" class="section level1">
+    <div id="phylogeneticem-1-0-1" class="section level1">
 <h1 class="hasAnchor">
-<a href="#phylogeneticem-1-0-0-900" class="anchor"></a>PhylogeneticEM 1.0.0.900</h1>
+<a href="#phylogeneticem-1-0-1" class="anchor"></a>PhylogeneticEM 1.0.1</h1>
 <ul>
 <li>Minor Changes:</li>
 <li>Impose a maximum value for alpha in find_grid_alpha to respect machine max double.</li>
+<li>New Features</li>
+<li>added argument <code>label_font</code> to <code>plot</code> function to control the label font.</li>
+<li>added argument <code>axis_las</code> to <code>plot</code> function to control the axis las.</li>
 <li>Bug fixes:</li>
 <li>Plotting missing values correctly in plot.PhyloEM.</li>
 <li>Bug fixes in plotting PhyloEM object when p = 1.</li>
 <li>When p=1 and nbr_alpha is not missing, do not switch to estimated mode for alpha.</li>
+<li>Technical:</li>
+<li>registration of c++ code to comply with R 3.4 new standards.</li>
 </ul>
 </div>
     <div id="phylogeneticem-1-0-0" class="section level1">
@@ -105,7 +110,7 @@ <h1 class="hasAnchor">
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#phylogeneticem-1-0-0-900">1.0.0.900</a></li>
+        <li><a href="#phylogeneticem-1-0-1">1.0.1</a></li>
         <li><a href="#phylogeneticem-1-0-0">1.0.0</a></li>
       </ul>
     </div>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index e704e06..9c437c7 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -36,11 +36,8 @@ img.icon {
 
 /* Section anchors ---------------------------------*/
 
-.hasAnchor {
-  margin-left: -30px;
-}
-
 a.anchor {
+  margin-left: -30px;
   display:inline-block;
   width: 30px;
   height: 30px;
@@ -56,6 +53,13 @@ a.anchor {
   visibility: visible;
 }
 
+@media (max-width: 767px) {
+  .hasAnchor:hover a.anchor {
+    visibility: hidden;
+  }
+}
+
+
 /* Fixes for fixed navbar --------------------------*/
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
@@ -63,6 +67,17 @@ a.anchor {
   margin-top: -60px;
 }
 
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+  .navbar-fixed-top {
+    position: absolute;
+  }
+  .navbar {
+    padding: 0;
+  }
+}
+
+
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -107,31 +122,33 @@ table {
 
 /* Syntax highlighting ---------------------------------------------------- */
 
-code {
-  background-color: #f7f7f7;
-  color: #333;
+pre {
+  word-wrap: normal;
+  word-break: normal;
+  border: 1px solid #eee;
 }
-code a {
-  color: #375f84;
-}
-
-.warning { color: red; }
-.message { font-weight: bolder; }
-.error   { color: red; font-weight: bolder; }
 
-.fl,.number {color:rgb(21,20,181);}
-.fu,.functioncall {color:#264D66 ;}
-.ch,.st,.string {color:#375D81 ;}
-.kw,.keyword {color:black;}
-.argument {color:#264D66 ;}
-.co,.comment {color: #777;}
-.formalargs {color: #264D66;}
-.eqformalargs {color:#264D66;}
-.slot {font-style:italic;}
-.symbol {color:black ;}
-.prompt {color:black ;}
+pre, code {
+  background-color: #f8f8f8;
+  color: #333;
+}
 
 pre img {
   background-color: #fff;
   display: block;
 }
+
+code a, pre a {
+  color: #375f84;
+}
+
+.fl      {color: #1514b5;}
+.fu      {color: #000000;} /* function */
+.ch,.st  {color: #036a07;} /* string */
+.kw      {color: #264D66;} /* keyword */
+.co      {color: #888888;} /* comment */
+
+.message { color: black;   font-weight: bolder;}
+.error   { color: orange;  font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
diff --git a/docs/reference/PhyloEM.html b/docs/reference/PhyloEM.html
index de3395f..6e51ffc 100644
--- a/docs/reference/PhyloEM.html
+++ b/docs/reference/PhyloEM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Model Estimation with Detection of Shifts</h1>
 This function can handle missing data.</p>
     
 
-    <pre><span class='fu'>PhyloEM</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>, <span class='st'>"rBM"</span>),
+    <pre class="usage"><span class='fu'>PhyloEM</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>, <span class='st'>"rBM"</span>),
   <span class='kw'>check_postorder</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>independent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>K_max</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fu'>floor</span>(<span class='fu'>sqrt</span>(<span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>))), <span class='fl'>10</span>),
   <span class='kw'>use_previous</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>order</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.selection</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"LINselect"</span>,
@@ -314,31 +314,31 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See a
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># ## Load Data</span>
-<span class='co'># data(monkeys)</span>
-<span class='co'># ## Run method</span>
-<span class='co'># # Note: use more alpha values for better results.</span>
-<span class='co'># res &lt;- PhyloEM(Y_data = monkeys$dat,        ## data</span>
-<span class='co'>#                phylo = monkeys$phy,         ## phylogeny</span>
-<span class='co'>#                process = "scOU",            ## scalar OU</span>
-<span class='co'>#                random.root = TRUE,          ## root is stationary</span>
-<span class='co'>#                stationary.root = TRUE,</span>
-<span class='co'>#                K_max = 10,                  ## maximal number of shifts</span>
-<span class='co'>#                nbr_alpha = 4,               ## number of alpha values</span>
-<span class='co'>#                parallel_alpha = TRUE,       ## parallelize on alpha values</span>
-<span class='co'>#                Ncores = 2)</span>
-<span class='co'># ## Plot selected solution (LINselect)</span>
-<span class='co'># plot(res) # three shifts</span>
-<span class='co'># ## Plot selected solution (DDSE)</span>
-<span class='co'># plot(res, method.selection = "DDSE") # no shift</span>
-<span class='co'># ## Extract and solution with 5 shifts</span>
-<span class='co'># params_5 &lt;- params_process(res, K = 5)</span>
-<span class='co'># plot(res, params = params_5)</span>
-<span class='co'># ## Show all equivalent solutions</span>
-<span class='co'># eq_sol &lt;- equivalent_shifts(monkeys$phy, params_5)</span>
-<span class='co'># plot(eq_sol)</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+    <pre class="examples"><div class='input'><span class='fu'>not_run</span>({
+  <span class='co'>## Load Data</span>
+  <span class='fu'>data</span>(<span class='no'>monkeys</span>)
+  <span class='co'>## Run method</span>
+  <span class='co'># Note: use more alpha values for better results.</span>
+  <span class='no'>res</span> <span class='kw'>&lt;-</span> <span class='fu'>PhyloEM</span>(<span class='kw'>Y_data</span> <span class='kw'>=</span> <span class='no'>monkeys</span>$<span class='no'>dat</span>,        <span class='co'>## data</span>
+                 <span class='kw'>phylo</span> <span class='kw'>=</span> <span class='no'>monkeys</span>$<span class='no'>phy</span>,         <span class='co'>## phylogeny</span>
+                 <span class='kw'>process</span> <span class='kw'>=</span> <span class='st'>"scOU"</span>,            <span class='co'>## scalar OU</span>
+                 <span class='kw'>random.root</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,          <span class='co'>## root is stationary</span>
+                 <span class='kw'>stationary.root</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+                 <span class='kw'>K_max</span> <span class='kw'>=</span> <span class='fl'>10</span>,                  <span class='co'>## maximal number of shifts</span>
+                 <span class='kw'>nbr_alpha</span> <span class='kw'>=</span> <span class='fl'>4</span>,               <span class='co'>## number of alpha values</span>
+                 <span class='kw'>parallel_alpha</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,       <span class='co'>## parallelize on alpha values</span>
+                 <span class='kw'>Ncores</span> <span class='kw'>=</span> <span class='fl'>2</span>)
+  <span class='co'>## Plot selected solution (LINselect)</span>
+  <span class='fu'>plot</span>(<span class='no'>res</span>) <span class='co'># three shifts</span>
+  <span class='co'>## Plot selected solution (DDSE)</span>
+  <span class='fu'>plot</span>(<span class='no'>res</span>, <span class='kw'>method.selection</span> <span class='kw'>=</span> <span class='st'>"DDSE"</span>) <span class='co'># no shift</span>
+  <span class='co'>## Extract and solution with 5 shifts</span>
+  <span class='no'>params_5</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='params_process.html'>params_process</a></span>(<span class='no'>res</span>, <span class='kw'>K</span> <span class='kw'>=</span> <span class='fl'>5</span>)
+  <span class='fu'>plot</span>(<span class='no'>res</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='no'>params_5</span>)
+  <span class='co'>## Show all equivalent solutions</span>
+  <span class='no'>eq_sol</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='equivalent_shifts.html'>equivalent_shifts</a></span>(<span class='no'>monkeys</span>$<span class='no'>phy</span>, <span class='no'>params_5</span>)
+  <span class='fu'>plot</span>(<span class='no'>eq_sol</span>)
+})</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/add_complementary.html b/docs/reference/add_complementary.html
index a970254..2fe7d57 100644
--- a/docs/reference/add_complementary.html
+++ b/docs/reference/add_complementary.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Add several entries, when only one is not NA.</h1>
     <p><code>add_complementary</code> return the only non NA value of a given vector.</p>
     
 
-    <pre><span class='fu'>add_complementary</span>(<span class='no'>z</span>)</pre>
+    <pre class="usage"><span class='fu'>add_complementary</span>(<span class='no'>z</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/allocate_regimes_from_shifts.html b/docs/reference/allocate_regimes_from_shifts.html
index db47760..069c594 100644
--- a/docs/reference/allocate_regimes_from_shifts.html
+++ b/docs/reference/allocate_regimes_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Allocation of regimes to nodes.</h1>
 i are numbered by i.</p>
     
 
-    <pre><span class='fu'>allocate_regimes_from_shifts</span>(<span class='no'>phylo</span>, <span class='no'>shifts_edges</span>)</pre>
+    <pre class="usage"><span class='fu'>allocate_regimes_from_shifts</span>(<span class='no'>phylo</span>, <span class='no'>shifts_edges</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/allocate_shifts_from_regimes.html b/docs/reference/allocate_shifts_from_regimes.html
index c14b7f5..9962483 100644
--- a/docs/reference/allocate_shifts_from_regimes.html
+++ b/docs/reference/allocate_shifts_from_regimes.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Allocation of shifts to edges</h1>
 by the allocation of the regimes. Only works in an "infinite site" model.</p>
     
 
-    <pre><span class='fu'>allocate_shifts_from_regimes</span>(<span class='no'>phylo</span>, <span class='no'>regimes</span>)</pre>
+    <pre class="usage"><span class='fu'>allocate_shifts_from_regimes</span>(<span class='no'>phylo</span>, <span class='no'>regimes</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/allocate_subset_node.simulate.html b/docs/reference/allocate_subset_node.simulate.html
index 7c836ab..0a3c1d7 100644
--- a/docs/reference/allocate_subset_node.simulate.html
+++ b/docs/reference/allocate_subset_node.simulate.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Iteration allocation</h1>
 To be used in function UpdateDown.</p>
     
 
-    <pre><span class='fu'>allocate_subset_node.simulate</span>(<span class='no'>node</span>, <span class='no'>array</span>, <span class='no'>value</span>)</pre>
+    <pre class="usage"><span class='fu'>allocate_subset_node.simulate</span>(<span class='no'>node</span>, <span class='no'>array</span>, <span class='no'>value</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/check.selection.strength.html b/docs/reference/check.selection.strength.html
index bcf3f29..f85fd53 100644
--- a/docs/reference/check.selection.strength.html
+++ b/docs/reference/check.selection.strength.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Check selection strength</h1>
 with a BM.</p>
     
 
-    <pre><span class='fu'>check.selection.strength</span>(<span class='no'>process</span>, <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>eps</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>6</span>),
+    <pre class="usage"><span class='fu'>check.selection.strength</span>(<span class='no'>process</span>, <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>eps</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>6</span>),
   <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/check_data.html b/docs/reference/check_data.html
index 167d36b..0ea08ac 100644
--- a/docs/reference/check_data.html
+++ b/docs/reference/check_data.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Test the format of data entry.</h1>
 correctly ordered to match the tips names.</p>
     
 
-    <pre><span class='fu'>check_data</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>check.tips.names</span>)</pre>
+    <pre class="usage"><span class='fu'>check_data</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>check.tips.names</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/check_dimensions.html b/docs/reference/check_dimensions.html
index 2e285c5..be4440f 100644
--- a/docs/reference/check_dimensions.html
+++ b/docs/reference/check_dimensions.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Check dimensions of the parameters</h1>
 If wrong, throw an error.</p>
     
 
-    <pre><span class='fu'>check_dimensions</span>(<span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='no'>variance</span>, <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+    <pre class="usage"><span class='fu'>check_dimensions</span>(<span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='no'>variance</span>, <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>optimal.value</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/check_parsimony.html b/docs/reference/check_parsimony.html
index dd3bb72..e273448 100644
--- a/docs/reference/check_parsimony.html
+++ b/docs/reference/check_parsimony.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Check Parsimony, assuming no homoplasy</h1>
 convergent regimes).</p>
     
 
-    <pre><span class='fu'>check_parsimony</span>(<span class='no'>tree</span>, <span class='no'>edges</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>check_parsimony</span>(<span class='no'>tree</span>, <span class='no'>edges</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/check_parsimony_clusters.html b/docs/reference/check_parsimony_clusters.html
index ff8c839..6e90419 100644
--- a/docs/reference/check_parsimony_clusters.html
+++ b/docs/reference/check_parsimony_clusters.html
@@ -26,7 +26,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -87,7 +87,7 @@ <h1>Check wether an allocation of the shifts is parsimonious,
 exactly the number of shifts plus one.</p>
     
 
-    <pre><span class='fu'>check_parsimony_clusters</span>(<span class='no'>tree</span>, <span class='no'>edges</span>, <span class='no'>clusters</span>)</pre>
+    <pre class="usage"><span class='fu'>check_parsimony_clusters</span>(<span class='no'>tree</span>, <span class='no'>edges</span>, <span class='no'>clusters</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/clusters_from_shifts.html b/docs/reference/clusters_from_shifts.html
index fbef8ce..4ad55a5 100644
--- a/docs/reference/clusters_from_shifts.html
+++ b/docs/reference/clusters_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Clustering associated to a shift allocation, assuming no homoplasy.</h1>
 convergence is allowed).</p>
     
 
-    <pre><span class='fu'>clusters_from_shifts</span>(<span class='no'>tree</span>, <span class='no'>edges</span>,
+    <pre class="usage"><span class='fu'>clusters_from_shifts</span>(<span class='no'>tree</span>, <span class='no'>edges</span>,
   <span class='kw'>part.list</span> <span class='kw'>=</span> <span class='fu'><a href='enumerate_tips_under_edges.html'>enumerate_tips_under_edges</a></span>(<span class='no'>tree</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_E.simple.html b/docs/reference/compute_E.simple.html
index 9e6ca97..fc759d6 100644
--- a/docs/reference/compute_E.simple.html
+++ b/docs/reference/compute_E.simple.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>E step</h1>
     <p><code>compute_E.simple</code> computes the E step in the simple case where the invert matrix Sigma_YY_inv is given</p>
     
 
-    <pre><span class='fu'>compute_E.simple</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>process</span>, <span class='no'>params_old</span>,
+    <pre class="usage"><span class='fu'>compute_E.simple</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>process</span>, <span class='no'>params_old</span>,
   <span class='kw'>masque_data</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fu'>rep</span>(<span class='fl'>TRUE</span>, <span class='fu'>attr</span>(<span class='no'>params_old</span>, <span class='st'>"p_dim"</span>) *
   <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)), <span class='fu'>rep</span>(<span class='fl'>FALSE</span>, <span class='fu'>attr</span>(<span class='no'>params_old</span>, <span class='st'>"p_dim"</span>) *
   <span class='no'>phylo</span>$<span class='no'>Nnode</span>)), <span class='no'>F_moments</span>, <span class='no'>Y_data_vec_known</span>, <span class='kw'>miss</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>FALSE</span>,
diff --git a/docs/reference/compute_actualization_matrix_ultrametric.html b/docs/reference/compute_actualization_matrix_ultrametric.html
index a28a86c..7ab3006 100644
--- a/docs/reference/compute_actualization_matrix_ultrametric.html
+++ b/docs/reference/compute_actualization_matrix_ultrametric.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute Matrix W of actualization (Ultrametric case)</h1>
 matrix of the (I_p - exp(-A * (h - t_pa(j))))_j node.</p>
     
 
-    <pre><span class='fu'>compute_actualization_matrix_ultrametric</span>(<span class='no'>tree</span>, <span class='no'>selection.strength</span>,
+    <pre class="usage"><span class='fu'>compute_actualization_matrix_ultrametric</span>(<span class='no'>tree</span>, <span class='no'>selection.strength</span>,
   <span class='kw'>times_shared</span> <span class='kw'>=</span> <span class='fu'><a href='compute_times_ca.html'>compute_times_ca</a></span>(<span class='no'>tree</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_betas_from_shifts.html b/docs/reference/compute_betas_from_shifts.html
index 234a986..83a0874 100644
--- a/docs/reference/compute_betas_from_shifts.html
+++ b/docs/reference/compute_betas_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Computation of the optimal values at nodes and tips.</h1>
 It assumes an OU model.</p>
     
 
-    <pre><span class='fu'>compute_betas_from_shifts</span>(<span class='no'>phylo</span>, <span class='no'>optimal.value</span>, <span class='no'>shifts</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_betas_from_shifts</span>(<span class='no'>phylo</span>, <span class='no'>optimal.value</span>, <span class='no'>shifts</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_diff_exp.BM.html b/docs/reference/compute_diff_exp.BM.html
index 330c3f6..c1468d1 100644
--- a/docs/reference/compute_diff_exp.BM.html
+++ b/docs/reference/compute_diff_exp.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute differences of expectations between node and parent.</h1>
 nodes and their parents.</p>
     
 
-    <pre><span class='fu'>compute_diff_exp.BM</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_diff_exp.BM</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_dist_phy.html b/docs/reference/compute_dist_phy.html
index 8067bc8..7474421 100644
--- a/docs/reference/compute_dist_phy.html
+++ b/docs/reference/compute_dist_phy.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Phylogenetic Distances</h1>
 tips i, j.</p>
     
 
-    <pre><span class='fu'>compute_dist_phy</span>(<span class='no'>phy</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_dist_phy</span>(<span class='no'>phy</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_expectations.BM.html b/docs/reference/compute_expectations.BM.html
index dd36cc2..b447936 100644
--- a/docs/reference/compute_expectations.BM.html
+++ b/docs/reference/compute_expectations.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute the expected states of a BM</h1>
 expected values at all the nodes.</p>
     
 
-    <pre><span class='fu'>compute_expectations.BM</span>(<span class='no'>phylo</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='kw'>U_tree</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_expectations.BM</span>(<span class='no'>phylo</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='kw'>U_tree</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_expectations.scOU.html b/docs/reference/compute_expectations.scOU.html
index 0848174..a8d10bf 100644
--- a/docs/reference/compute_expectations.scOU.html
+++ b/docs/reference/compute_expectations.scOU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute the expected states of a scOU</h1>
 expected values at all the nodes. Assumes a stationary root.</p>
     
 
-    <pre><span class='fu'>compute_expectations.scOU</span>(<span class='no'>phylo</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='no'>alpha</span>, <span class='kw'>U_tree</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+    <pre class="usage"><span class='fu'>compute_expectations.scOU</span>(<span class='no'>phylo</span>, <span class='no'>root.state</span>, <span class='no'>shifts</span>, <span class='no'>alpha</span>, <span class='kw'>U_tree</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>times_shared</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_fixed_moments.html b/docs/reference/compute_fixed_moments.html
index d5d15a4..e2aff1c 100644
--- a/docs/reference/compute_fixed_moments.html
+++ b/docs/reference/compute_fixed_moments.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute fixed moments for E step.</h1>
 there is no missing data.</p>
     
 
-    <pre><span class='fu'>compute_fixed_moments</span>(<span class='no'>times_shared</span>, <span class='no'>ntaxa</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_fixed_moments</span>(<span class='no'>times_shared</span>, <span class='no'>ntaxa</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_gauss_lasso.html b/docs/reference/compute_gauss_lasso.html
index a6fc42e..c2cd8b5 100644
--- a/docs/reference/compute_gauss_lasso.html
+++ b/docs/reference/compute_gauss_lasso.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Do a lm on top of a lasso regression.</h1>
 transformed data (root = an integer).</p>
     
 
-    <pre><span class='fu'>compute_gauss_lasso</span>(<span class='no'>Ypt</span>, <span class='no'>Xp</span>, <span class='no'>delta</span>, <span class='no'>root</span>, <span class='kw'>projection</span> <span class='kw'>=</span> <span class='fu'>which</span>(<span class='fu'>rowSums</span>(<span class='no'>delta</span>) <span class='kw'>!=</span>
+    <pre class="usage"><span class='fu'>compute_gauss_lasso</span>(<span class='no'>Ypt</span>, <span class='no'>Xp</span>, <span class='no'>delta</span>, <span class='no'>root</span>, <span class='kw'>projection</span> <span class='kw'>=</span> <span class='fu'>which</span>(<span class='fu'>rowSums</span>(<span class='no'>delta</span>) <span class='kw'>!=</span>
   <span class='fl'>0</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_log_likelihood.simple.html b/docs/reference/compute_log_likelihood.simple.html
index 11b3b20..dbde031 100644
--- a/docs/reference/compute_log_likelihood.simple.html
+++ b/docs/reference/compute_log_likelihood.simple.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Log Likelihood</h1>
 in the simple case where the inverse of the variance matrix is given.</p>
     
 
-    <pre><span class='fu'>compute_log_likelihood.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma</span>, <span class='no'>Sigma_YY_chol_inv</span>,
+    <pre class="usage"><span class='fu'>compute_log_likelihood.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma</span>, <span class='no'>Sigma_YY_chol_inv</span>,
   <span class='kw'>miss</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>FALSE</span>, <span class='fu'>dim</span>(<span class='no'>sim</span>)[<span class='fl'>1</span>] * <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)),
   <span class='kw'>masque_data</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fu'>rep</span>(<span class='fl'>TRUE</span>, <span class='fu'>dim</span>(<span class='no'>sim</span>)[<span class='fl'>1</span>] * <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)), <span class='fu'>rep</span>(<span class='fl'>FALSE</span>,
   <span class='fu'>dim</span>(<span class='no'>sim</span>)[<span class='fl'>1</span>] * <span class='no'>phylo</span>$<span class='no'>Nnode</span>)), <span class='no'>...</span>)</pre>
diff --git a/docs/reference/compute_mahalanobis_distance.simple.html b/docs/reference/compute_mahalanobis_distance.simple.html
index 92b0f0c..e05e868 100644
--- a/docs/reference/compute_mahalanobis_distance.simple.html
+++ b/docs/reference/compute_mahalanobis_distance.simple.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Squared Mahalanobis Distance</h1>
 of the variance matrix is given.</p>
     
 
-    <pre><span class='fu'>compute_mahalanobis_distance.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma_YY_chol_inv</span>,
+    <pre class="usage"><span class='fu'>compute_mahalanobis_distance.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma_YY_chol_inv</span>,
   <span class='kw'>miss</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>FALSE</span>, <span class='fu'>dim</span>(<span class='no'>sim</span>)[<span class='fl'>1</span>] * <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)), <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_mean_variance.simple.html b/docs/reference/compute_mean_variance.simple.html
index 8ba5b1c..5344672 100644
--- a/docs/reference/compute_mean_variance.simple.html
+++ b/docs/reference/compute_mean_variance.simple.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute moments of params_old</h1>
 mean and variance matrix with parameters params_old.</p>
     
 
-    <pre><span class='fu'>compute_mean_variance.simple</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>,
+    <pre class="usage"><span class='fu'>compute_mean_variance.simple</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>,
   <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"rBM"</span>, <span class='st'>"scOU"</span>), <span class='no'>params_old</span>,
   <span class='kw'>masque_data</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fu'>rep</span>(<span class='fl'>TRUE</span>, <span class='fu'>attr</span>(<span class='no'>params_old</span>, <span class='st'>"p_dim"</span>) *
   <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)), <span class='fu'>rep</span>(<span class='fl'>FALSE</span>, <span class='fu'>attr</span>(<span class='no'>params_old</span>, <span class='st'>"p_dim"</span>) *
diff --git a/docs/reference/compute_residuals.simple.html b/docs/reference/compute_residuals.simple.html
index b70953a..f152756 100644
--- a/docs/reference/compute_residuals.simple.html
+++ b/docs/reference/compute_residuals.simple.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Residuals</h1>
 data in the simple case where the inverse of the variance matrix is given.</p>
     
 
-    <pre><span class='fu'>compute_residuals.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma_YY_chol_inv</span>, <span class='no'>miss</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_residuals.simple</span>(<span class='no'>phylo</span>, <span class='no'>Y_data_vec</span>, <span class='no'>sim</span>, <span class='no'>Sigma_YY_chol_inv</span>, <span class='no'>miss</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_shifts_from_betas.html b/docs/reference/compute_shifts_from_betas.html
index dd098d7..ab0a91a 100644
--- a/docs/reference/compute_shifts_from_betas.html
+++ b/docs/reference/compute_shifts_from_betas.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Computation of shifts from the vector of optimal values</h1>
 to the vector of optimal values on nodes.</p>
     
 
-    <pre><span class='fu'>compute_shifts_from_betas</span>(<span class='no'>phylo</span>, <span class='no'>betas</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_shifts_from_betas</span>(<span class='no'>phylo</span>, <span class='no'>betas</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_state_filter.html b/docs/reference/compute_state_filter.html
index 442833b..227a0e3 100644
--- a/docs/reference/compute_state_filter.html
+++ b/docs/reference/compute_state_filter.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>List of potential daughter states when parent is in state k.</h1>
 the parent node is in state k.</p>
     
 
-    <pre><span class='fu'>compute_state_filter</span>(<span class='no'>cost</span>, <span class='no'>k</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_state_filter</span>(<span class='no'>cost</span>, <span class='no'>k</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_stationary_variance.html b/docs/reference/compute_stationary_variance.html
index cad63cb..6a7886d 100644
--- a/docs/reference/compute_stationary_variance.html
+++ b/docs/reference/compute_stationary_variance.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute the stationary variance matrix</h1>
 an OU process.</p>
     
 
-    <pre><span class='fu'>compute_stationary_variance</span>(<span class='no'>variance</span>, <span class='no'>selection.strength</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_stationary_variance</span>(<span class='no'>variance</span>, <span class='no'>selection.strength</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_sum_var_diff.html b/docs/reference/compute_sum_var_diff.html
index d3371b3..382b7a8 100644
--- a/docs/reference/compute_sum_var_diff.html
+++ b/docs/reference/compute_sum_var_diff.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Compute weighted sum of var_diff</h1>
     <p><code>compute_sum_var_diff</code> computes sum_e edge ell_j * Var[X_j - X_pa(j) | Y]</p>
     
 
-    <pre><span class='fu'>compute_sum_var_diff</span>(<span class='no'>phylo</span>, <span class='no'>var_diff</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_sum_var_diff</span>(<span class='no'>phylo</span>, <span class='no'>var_diff</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_times_ca.html b/docs/reference/compute_times_ca.html
index cc2453f..489bb15 100644
--- a/docs/reference/compute_times_ca.html
+++ b/docs/reference/compute_times_ca.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Comon Ancestors Times</h1>
 ancestor of two tips i, j.</p>
     
 
-    <pre><span class='fu'>compute_times_ca</span>(<span class='no'>phy</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_times_ca</span>(<span class='no'>phy</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_tree_correlations_matrix.BM.html b/docs/reference/compute_tree_correlations_matrix.BM.html
index 792e0f2..1957099 100644
--- a/docs/reference/compute_tree_correlations_matrix.BM.html
+++ b/docs/reference/compute_tree_correlations_matrix.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Matrix of tree-induced correlations for the BM</h1>
     <p><code>compute_tree_correlations_matrix.BM</code> returns times_shared its provided argument.</p>
     
 
-    <pre><span class='fu'>compute_tree_correlations_matrix.BM</span>(<span class='no'>times_shared</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_tree_correlations_matrix.BM</span>(<span class='no'>times_shared</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_tree_correlations_matrix.scOU.html b/docs/reference/compute_tree_correlations_matrix.scOU.html
index 1f3a220..aa72dfa 100644
--- a/docs/reference/compute_tree_correlations_matrix.scOU.html
+++ b/docs/reference/compute_tree_correlations_matrix.scOU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Matrix of tree-induced correlations for the scOU</h1>
 state.</p>
     
 
-    <pre><span class='fu'>compute_tree_correlations_matrix.scOU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>,
+    <pre class="usage"><span class='fu'>compute_tree_correlations_matrix.scOU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>,
   <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/compute_var_M.BM.html b/docs/reference/compute_var_M.BM.html
index 1f14758..d25c314 100644
--- a/docs/reference/compute_var_M.BM.html
+++ b/docs/reference/compute_var_M.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Computation of the variance.</h1>
     <p><code>compute_var_M.BM</code> finds the variance that is the maximum of likelihood</p>
     
 
-    <pre><span class='fu'>compute_var_M.BM</span>(<span class='no'>phylo</span>, <span class='no'>var_diff</span>, <span class='no'>diff_exp</span>, <span class='no'>edges_max</span>, <span class='no'>random.root</span>, <span class='no'>mu</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_var_M.BM</span>(<span class='no'>phylo</span>, <span class='no'>var_diff</span>, <span class='no'>diff_exp</span>, <span class='no'>edges_max</span>, <span class='no'>random.root</span>, <span class='no'>mu</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_var_diff.BM.html b/docs/reference/compute_var_diff.BM.html
index 30b80b5..8ce957c 100644
--- a/docs/reference/compute_var_diff.BM.html
+++ b/docs/reference/compute_var_diff.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute variances of differences between nodes and parents.</h1>
 nodes and their parents.</p>
     
 
-    <pre><span class='fu'>compute_var_diff.BM</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_var_diff.BM</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_variance_covariance.BM.html b/docs/reference/compute_variance_covariance.BM.html
index 85d9fd0..9736daf 100644
--- a/docs/reference/compute_variance_covariance.BM.html
+++ b/docs/reference/compute_variance_covariance.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Complete variance covariance matrix for BM</h1>
 matrix of vec(X).</p>
     
 
-    <pre><span class='fu'>compute_variance_covariance.BM</span>(<span class='no'>times_shared</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_variance_covariance.BM</span>(<span class='no'>times_shared</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_variance_covariance.OU.html b/docs/reference/compute_variance_covariance.OU.html
index 9550952..7823653 100644
--- a/docs/reference/compute_variance_covariance.OU.html
+++ b/docs/reference/compute_variance_covariance.OU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Complete variance covariance matrix for OU</h1>
 covariance matrix of vec(X).</p>
     
 
-    <pre><span class='fu'>compute_variance_covariance.OU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_variance_covariance.OU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/compute_variance_covariance.scOU.html b/docs/reference/compute_variance_covariance.scOU.html
index 3bb9401..b3812bb 100644
--- a/docs/reference/compute_variance_covariance.scOU.html
+++ b/docs/reference/compute_variance_covariance.scOU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Complete variance covariance matrix for scOU</h1>
 matrix of vec(X).</p>
     
 
-    <pre><span class='fu'>compute_variance_covariance.scOU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>compute_variance_covariance.scOU</span>(<span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>params_old</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/correspondenceEdges.html b/docs/reference/correspondenceEdges.html
index 6c45653..869a4de 100644
--- a/docs/reference/correspondenceEdges.html
+++ b/docs/reference/correspondenceEdges.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Correspondence between edges numbers</h1>
 their corresponding numbers on the output tree.</p>
     
 
-    <pre><span class='fu'>correspondenceEdges</span>(<span class='no'>edges</span>, <span class='no'>from</span>, <span class='no'>to</span>)</pre>
+    <pre class="usage"><span class='fu'>correspondenceEdges</span>(<span class='no'>edges</span>, <span class='no'>from</span>, <span class='no'>to</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/enlight.html b/docs/reference/enlight.html
index 3bfefbf..d6cb0f1 100644
--- a/docs/reference/enlight.html
+++ b/docs/reference/enlight.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Make the result lighter</h1>
 re-computed using function <code><a href='imputed_traits.html'>imputed_traits.PhyloEM</a></code>.</p>
     
 
-    <pre><span class='fu'>enlight</span>(<span class='no'>x</span>)
+    <pre class="usage"><span class='fu'>enlight</span>(<span class='no'>x</span>)
 
 <span class='co'># S3 method for PhyloEM</span>
 <span class='fu'>enlight</span>(<span class='no'>x</span>)</pre>
diff --git a/docs/reference/enumerate_parsimony-2.png b/docs/reference/enumerate_parsimony-2.png
index 9fcb9d5..75bc1e6 100644
Binary files a/docs/reference/enumerate_parsimony-2.png and b/docs/reference/enumerate_parsimony-2.png differ
diff --git a/docs/reference/enumerate_parsimony-4.png b/docs/reference/enumerate_parsimony-4.png
index 29da3c2..01b5ccc 100644
Binary files a/docs/reference/enumerate_parsimony-4.png and b/docs/reference/enumerate_parsimony-4.png differ
diff --git a/docs/reference/enumerate_parsimony.html b/docs/reference/enumerate_parsimony.html
index 085270f..bda3d5b 100644
--- a/docs/reference/enumerate_parsimony.html
+++ b/docs/reference/enumerate_parsimony.html
@@ -26,7 +26,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -87,7 +87,7 @@ <h1>Enumerate all the possible regime allocations, given a culstering
 equivalent regimes is given by <code><a href='parsimonyNumber.html'>parsimonyNumber</a></code> (which is faster).</p>
     
 
-    <pre><span class='fu'>enumerate_parsimony</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
+    <pre class="usage"><span class='fu'>enumerate_parsimony</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/enumerate_tips_under_edges.html b/docs/reference/enumerate_tips_under_edges.html
index 2510377..1771e5d 100644
--- a/docs/reference/enumerate_tips_under_edges.html
+++ b/docs/reference/enumerate_tips_under_edges.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Tips descendants of nodes.</h1>
 of the tips that have this edge as an ancestor.</p>
     
 
-    <pre><span class='fu'>enumerate_tips_under_edges</span>(<span class='no'>tree</span>)</pre>
+    <pre class="usage"><span class='fu'>enumerate_tips_under_edges</span>(<span class='no'>tree</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/equivalent_shifts-14.png b/docs/reference/equivalent_shifts-14.png
index 6257c32..871aff8 100644
Binary files a/docs/reference/equivalent_shifts-14.png and b/docs/reference/equivalent_shifts-14.png differ
diff --git a/docs/reference/equivalent_shifts-4.png b/docs/reference/equivalent_shifts-4.png
index 1d4231d..b2dd5e1 100644
Binary files a/docs/reference/equivalent_shifts-4.png and b/docs/reference/equivalent_shifts-4.png differ
diff --git a/docs/reference/equivalent_shifts.html b/docs/reference/equivalent_shifts.html
index 869fd89..554b9db 100644
--- a/docs/reference/equivalent_shifts.html
+++ b/docs/reference/equivalent_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Find all equivalent shifts allocations and values.</h1>
 corresponding values, assuming an ultrametric tree.</p>
     
 
-    <pre><span class='fu'>equivalent_shifts</span>(<span class='no'>phylo</span>, <span class='no'>params</span>, <span class='kw'>T_tree</span> <span class='kw'>=</span> <span class='fu'><a href='incidence.matrix.html'>incidence.matrix</a></span>(<span class='no'>phylo</span>),
+    <pre class="usage"><span class='fu'>equivalent_shifts</span>(<span class='no'>phylo</span>, <span class='no'>params</span>, <span class='kw'>T_tree</span> <span class='kw'>=</span> <span class='fu'><a href='incidence.matrix.html'>incidence.matrix</a></span>(<span class='no'>phylo</span>),
   <span class='kw'>part.list</span> <span class='kw'>=</span> <span class='fu'><a href='enumerate_tips_under_edges.html'>enumerate_tips_under_edges</a></span>(<span class='no'>phylo</span>), <span class='kw'>times_shared</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/equivalent_shifts_edges.html b/docs/reference/equivalent_shifts_edges.html
index b502386..a5470af 100644
--- a/docs/reference/equivalent_shifts_edges.html
+++ b/docs/reference/equivalent_shifts_edges.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Find all the equivalent shift edges allocations.</h1>
 to find all the shifts positions that are equivalent to a given one.</p>
     
 
-    <pre><span class='fu'>equivalent_shifts_edges</span>(<span class='no'>phylo</span>, <span class='no'>shifts_edges</span>,
+    <pre class="usage"><span class='fu'>equivalent_shifts_edges</span>(<span class='no'>phylo</span>, <span class='no'>shifts_edges</span>,
   <span class='kw'>part.list</span> <span class='kw'>=</span> <span class='fu'><a href='enumerate_tips_under_edges.html'>enumerate_tips_under_edges</a></span>(<span class='no'>phylo</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/equivalent_shifts_values.html b/docs/reference/equivalent_shifts_values.html
index 5056b4c..24d90ff 100644
--- a/docs/reference/equivalent_shifts_values.html
+++ b/docs/reference/equivalent_shifts_values.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Find values given edges. OU stationary case. Ultrametric tree.</h1>
 <code><a href='equivalent_shifts_edges.html'>equivalent_shifts_edges</a></code>.</p>
     
 
-    <pre><span class='fu'>equivalent_shifts_values</span>(<span class='no'>phylo</span>, <span class='no'>eq_shifts_edges</span>, <span class='no'>T_tree_ac</span>, <span class='no'>vect_Y</span>, <span class='no'>p</span>)</pre>
+    <pre class="usage"><span class='fu'>equivalent_shifts_values</span>(<span class='no'>phylo</span>, <span class='no'>eq_shifts_edges</span>, <span class='no'>T_tree_ac</span>, <span class='no'>vect_Y</span>, <span class='no'>p</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/estimate.alpha.html b/docs/reference/estimate.alpha.html
index da4455a..173abab 100644
--- a/docs/reference/estimate.alpha.html
+++ b/docs/reference/estimate.alpha.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Function to estimate alpha</h1>
 alpha_old is not far from reality.</p>
     
 
-    <pre><span class='fu'>estimate.alpha</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>, <span class='no'>sigma2</span>, <span class='no'>mu</span>, <span class='no'>shifts</span>, <span class='no'>alpha_old</span>,
+    <pre class="usage"><span class='fu'>estimate.alpha</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>, <span class='no'>sigma2</span>, <span class='no'>mu</span>, <span class='no'>shifts</span>, <span class='no'>alpha_old</span>,
   <span class='no'>max_selection.strength</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/estimateEM.html b/docs/reference/estimateEM.html
index 850e431..2ffae7c 100644
--- a/docs/reference/estimateEM.html
+++ b/docs/reference/estimateEM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Perform One EM</h1>
 should not need it.</p>
     
 
-    <pre><span class='fu'>estimateEM</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>Y_data_imp</span> <span class='kw'>=</span> <span class='no'>Y_data</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>,
+    <pre class="usage"><span class='fu'>estimateEM</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>Y_data_imp</span> <span class='kw'>=</span> <span class='no'>Y_data</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>,
   <span class='st'>"scOU"</span>, <span class='st'>"rBM"</span>), <span class='kw'>independent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>variance</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>),
   <span class='kw'>value.root</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>), <span class='kw'>exp.root</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>), <span class='kw'>var.root</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>),
   <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>), <span class='kw'>normalized_half_life</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>2</span>), <span class='kw'>log_likelihood</span> <span class='kw'>=</span>
diff --git a/docs/reference/extract.enumerate_parsimony.html b/docs/reference/extract.enumerate_parsimony.html
index 23ba3c2..9be5978 100644
--- a/docs/reference/extract.enumerate_parsimony.html
+++ b/docs/reference/extract.enumerate_parsimony.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Extract the result of <code>enumerate_parsimony</code> at a node.</h1>
 possible regime allocations for the nodes of a given subtree.</p>
     
 
-    <pre><span class='co'># S3 method for enumerate_parsimony</span>
+    <pre class="usage"><span class='co'># S3 method for enumerate_parsimony</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>node</span> <span class='kw'>=</span> <span class='fu'>attr</span>(<span class='no'>x</span>$<span class='no'>allocations</span>, <span class='st'>"ntaxa"</span>) +
   <span class='fl'>1</span>, <span class='kw'>what</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"solutions"</span>, <span class='st'>"number"</span>, <span class='st'>"cost"</span>), <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/extract.equivalent_shifts.html b/docs/reference/extract.equivalent_shifts.html
index d4273d7..1c74987 100644
--- a/docs/reference/extract.equivalent_shifts.html
+++ b/docs/reference/extract.equivalent_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Extract the shifts values for one trait.</h1>
 and returns the shifts of root values for a given trait.</p>
     
 
-    <pre><span class='co'># S3 method for equivalent_shifts</span>
+    <pre class="usage"><span class='co'># S3 method for equivalent_shifts</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>what</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"shifts_values"</span>,
   <span class='st'>"root_values"</span>), <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/extract.html b/docs/reference/extract.html
index b19a341..806c003 100644
--- a/docs/reference/extract.html
+++ b/docs/reference/extract.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Extraction function</h1>
     <p><code>extract</code> the needed quantities out of an S3 object.</p>
     
 
-    <pre><span class='fu'>extract</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>extract</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/extract.parsimonyCost.html b/docs/reference/extract.parsimonyCost.html
index e35e904..49c998d 100644
--- a/docs/reference/extract.parsimonyCost.html
+++ b/docs/reference/extract.parsimonyCost.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Extraction of the actual number of solutions.</h1>
 at the given node.</p>
     
 
-    <pre><span class='co'># S3 method for parsimonyCost</span>
+    <pre class="usage"><span class='co'># S3 method for parsimonyCost</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>node</span> <span class='kw'>=</span> <span class='fu'>attr</span>(<span class='no'>x</span>, <span class='st'>"ntaxa"</span>) + <span class='fl'>1</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/extract.parsimonyNumber.html b/docs/reference/extract.parsimonyNumber.html
index ef560ef..481d6a6 100644
--- a/docs/reference/extract.parsimonyNumber.html
+++ b/docs/reference/extract.parsimonyNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Extraction of the actual number of solutions.</h1>
 solution for any subtree starting from a given node.</p>
     
 
-    <pre><span class='co'># S3 method for parsimonyNumber</span>
+    <pre class="usage"><span class='co'># S3 method for parsimonyNumber</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>node</span> <span class='kw'>=</span> <span class='fu'>attr</span>(<span class='no'>x</span>$<span class='no'>nbrReconstructions</span>,
   <span class='st'>"ntaxa"</span>) + <span class='fl'>1</span>, <span class='kw'>what</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"number"</span>, <span class='st'>"cost"</span>), <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/extract.partitionsNumber.html b/docs/reference/extract.partitionsNumber.html
index ba77e1e..c848e2e 100644
--- a/docs/reference/extract.partitionsNumber.html
+++ b/docs/reference/extract.partitionsNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Extract from object <code>partitionsNumber</code></h1>
 given sub-tree, either marked or non-marked.</p>
     
 
-    <pre><span class='co'># S3 method for partitionsNumber</span>
+    <pre class="usage"><span class='co'># S3 method for partitionsNumber</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>node</span> <span class='kw'>=</span> <span class='fu'>attr</span>(<span class='no'>x</span>, <span class='st'>"ntaxa"</span>) + <span class='fl'>1</span>,
   <span class='kw'>npart</span> <span class='kw'>=</span> <span class='fu'>attr</span>(<span class='no'>x</span>, <span class='st'>"npart"</span>), <span class='kw'>marqued</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/extract.simul_process.html b/docs/reference/extract.simul_process.html
index 3be3023..b6425b6 100644
--- a/docs/reference/extract.simul_process.html
+++ b/docs/reference/extract.simul_process.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Extraction of simulated traits</h1>
 expectations or optimal values at the tips or the internal nodes.</p>
     
 
-    <pre><span class='co'># S3 method for simul_process</span>
+    <pre class="usage"><span class='co'># S3 method for simul_process</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>x</span>, <span class='kw'>where</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"tips"</span>, <span class='st'>"nodes"</span>),
   <span class='kw'>what</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"states"</span>, <span class='st'>"expectations"</span>, <span class='st'>"optimal.values"</span>), <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/extract.variance_covariance.html b/docs/reference/extract.variance_covariance.html
index 0e651bd..a349290 100644
--- a/docs/reference/extract.variance_covariance.html
+++ b/docs/reference/extract.variance_covariance.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Extract sub-matrices of variance.</h1>
     <p><code>extract.variance_covariance</code> return the adequate sub-matrix.</p>
     
 
-    <pre><span class='co'># S3 method for variance_covariance</span>
+    <pre class="usage"><span class='co'># S3 method for variance_covariance</span>
 <span class='fu'><a href='extract.html'>extract</a></span>(<span class='no'>struct</span>, <span class='kw'>what</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"YY"</span>, <span class='st'>"YZ"</span>, <span class='st'>"ZZ"</span>),
   <span class='kw'>masque_data</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fu'>rep</span>(<span class='fl'>TRUE</span>, <span class='fu'>attr</span>(<span class='no'>struct</span>, <span class='st'>"ntaxa"</span>) * <span class='fu'>attr</span>(<span class='no'>struct</span>, <span class='st'>"p_dim"</span>)),
   <span class='fu'>rep</span>(<span class='fl'>FALSE</span>, (<span class='fu'>dim</span>(<span class='no'>struct</span>)[<span class='fl'>1</span>] - <span class='fu'>attr</span>(<span class='no'>struct</span>, <span class='st'>"ntaxa"</span>)) * <span class='fu'>attr</span>(<span class='no'>struct</span>, <span class='st'>"p_dim"</span>))))</pre>
diff --git a/docs/reference/find_grid_alpha.html b/docs/reference/find_grid_alpha.html
index 0ff733f..5230c54 100644
--- a/docs/reference/find_grid_alpha.html
+++ b/docs/reference/find_grid_alpha.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Find a reasonable grid for alpha</h1>
 almost all the tips are decorrelated.</p>
     
 
-    <pre><span class='fu'>find_grid_alpha</span>(<span class='no'>phy</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nbr_alpha</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>factor_up_alpha</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+    <pre class="usage"><span class='fu'>find_grid_alpha</span>(<span class='no'>phy</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nbr_alpha</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>factor_up_alpha</span> <span class='kw'>=</span> <span class='fl'>2</span>,
   <span class='kw'>factor_down_alpha</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>quantile_low_distance</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>,
   <span class='kw'>log_transform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html b/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html
index 0da57d6..a1968ba 100644
--- a/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html
+++ b/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Given a regularization path, find K selected independant variables.</h1>
 are selected, so that the selected columns of matrix Xp are independant.</p>
     
 
-    <pre><span class='fu'>find_independent_regression_vectors.glmnet_multivariate</span>(<span class='no'>Xp</span>, <span class='no'>K</span>, <span class='no'>fit</span>, <span class='no'>root</span>)</pre>
+    <pre class="usage"><span class='fu'>find_independent_regression_vectors.glmnet_multivariate</span>(<span class='no'>Xp</span>, <span class='no'>K</span>, <span class='no'>fit</span>, <span class='no'>root</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/find_shift_values.html b/docs/reference/find_shift_values.html
index dffb72c..d30d5c1 100644
--- a/docs/reference/find_shift_values.html
+++ b/docs/reference/find_shift_values.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Find values given edges. OU stationary case. Ultrametric tree.</h1>
 shifts postions and the mean values are compatible.</p>
     
 
-    <pre><span class='fu'>find_shift_values</span>(<span class='no'>shifts_edges</span>, <span class='no'>T_tree_ac</span>, <span class='no'>vect_Y</span>, <span class='no'>p</span>, <span class='no'>ntaxa</span>)</pre>
+    <pre class="usage"><span class='fu'>find_shift_values</span>(<span class='no'>shifts_edges</span>, <span class='no'>T_tree_ac</span>, <span class='no'>vect_Y</span>, <span class='no'>p</span>, <span class='no'>ntaxa</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/format_output.html b/docs/reference/format_output.html
index 90a52f1..1581445 100644
--- a/docs/reference/format_output.html
+++ b/docs/reference/format_output.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Run the EM for several values of K</h1>
 for all values of K between 0 and K_max.</p>
     
 
-    <pre><span class='fu'>format_output</span>(<span class='no'>results_estim_EM</span>, <span class='no'>phylo</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+    <pre class="usage"><span class='fu'>format_output</span>(<span class='no'>results_estim_EM</span>, <span class='no'>phylo</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/get_variance_node.html b/docs/reference/get_variance_node.html
index 9ce0cc5..49136d5 100644
--- a/docs/reference/get_variance_node.html
+++ b/docs/reference/get_variance_node.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Get variance matrix of a node</h1>
 corariance of a node and its parent.</p>
     
 
-    <pre><span class='fu'>get_variance_node</span>(<span class='no'>node</span>, <span class='no'>vars</span>)</pre>
+    <pre class="usage"><span class='fu'>get_variance_node</span>(<span class='no'>node</span>, <span class='no'>vars</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/go_back_to_original_process.html b/docs/reference/go_back_to_original_process.html
index 22ab41b..215a03b 100644
--- a/docs/reference/go_back_to_original_process.html
+++ b/docs/reference/go_back_to_original_process.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Scale the parameters back to the original process</h1>
 the original process.</p>
     
 
-    <pre><span class='fu'>go_back_to_original_process</span>(<span class='no'>phy_original</span>, <span class='no'>known.selection.strength</span>,
+    <pre class="usage"><span class='fu'>go_back_to_original_process</span>(<span class='no'>phy_original</span>, <span class='no'>known.selection.strength</span>,
   <span class='no'>sBM_variance</span>, <span class='no'>params</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/impute.data.Rphylopars.html b/docs/reference/impute.data.Rphylopars.html
index 2ff6384..f34d5f2 100644
--- a/docs/reference/impute.data.Rphylopars.html
+++ b/docs/reference/impute.data.Rphylopars.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initial imputation of missing data for lasso</h1>
 to impute missing data.</p>
     
 
-    <pre><span class='fu'>impute.data.Rphylopars</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>process</span>, <span class='no'>random.init</span>)</pre>
+    <pre class="usage"><span class='fu'>impute.data.Rphylopars</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>process</span>, <span class='no'>random.init</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/imputed_traits.html b/docs/reference/imputed_traits.html
index afe6d66..6cae21d 100644
--- a/docs/reference/imputed_traits.html
+++ b/docs/reference/imputed_traits.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Ancestral State Reconstruction</h1>
 state reconstruction) or at the tips (data imputation)</p>
     
 
-    <pre><span class='fu'>imputed_traits</span>(<span class='no'>x</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>imputed_traits</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for PhyloEM</span>
 <span class='fu'>imputed_traits</span>(<span class='no'>x</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>save_all</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
diff --git a/docs/reference/incidence.matrix.full.html b/docs/reference/incidence.matrix.full.html
index de62bdb..720dee0 100644
--- a/docs/reference/incidence.matrix.full.html
+++ b/docs/reference/incidence.matrix.full.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Incidence matrix of a tree.</h1>
 otherwise.</p>
     
 
-    <pre><span class='fu'>incidence.matrix.full</span>(<span class='no'>phylo</span>)</pre>
+    <pre class="usage"><span class='fu'>incidence.matrix.full</span>(<span class='no'>phylo</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/incidence.matrix.html b/docs/reference/incidence.matrix.html
index 558847e..55f7e75 100644
--- a/docs/reference/incidence.matrix.html
+++ b/docs/reference/incidence.matrix.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Incidence matrix of a tree.</h1>
 otherwise.</p>
     
 
-    <pre><span class='fu'>incidence.matrix</span>(<span class='no'>phylo</span>)</pre>
+    <pre class="usage"><span class='fu'>incidence.matrix</span>(<span class='no'>phylo</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/incidence_matrix_actualization_factors.html b/docs/reference/incidence_matrix_actualization_factors.html
index ea007d3..1b07208 100644
--- a/docs/reference/incidence_matrix_actualization_factors.html
+++ b/docs/reference/incidence_matrix_actualization_factors.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Compute the actualizations factors to apply to the incidence matrix.</h1>
 This matrix is to be multiplied to the incidence matrix with an outer product.</p>
     
 
-    <pre><span class='fu'>incidence_matrix_actualization_factors</span>(<span class='no'>tree</span>, <span class='no'>selection.strength</span>,
+    <pre class="usage"><span class='fu'>incidence_matrix_actualization_factors</span>(<span class='no'>tree</span>, <span class='no'>selection.strength</span>,
   <span class='kw'>relativeTimes_tree</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>times_shared</span> <span class='kw'>=</span> <span class='fu'><a href='compute_times_ca.html'>compute_times_ca</a></span>(<span class='no'>tree</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b7b6e99..5e30e3f 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -78,7 +78,7 @@
     <div class="page-header">
       <h1>
         Reference
-        <small>version&nbsp;1.0.0.9000</small>
+        <small>version&nbsp;1.0.1</small>
       </h1>
     </div>
 
@@ -126,43 +126,43 @@ <h2 id="section-phyloem-handling-functions" class="hasAnchor"><a href="#section-
         <tr>
           <!--  -->
           <td>
-            <p><code><a href="plot.PhyloEM.html">plot.PhyloEM</a></code> </p>
+            <p><code><a href="plot.PhyloEM.html">plot</a></code> </p>
           </td>
           <td><p>Plot for class <code>PhyloEM</code></p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="params_process.PhyloEM.html">params_process.PhyloEM</a></code> </p>
+            <p><code><a href="params_process.PhyloEM.html">params_process</a></code> </p>
           </td>
           <td><p>Parameter estimates</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="imputed_traits.html">imputed_traits</a></code> <code><a href="imputed_traits.html">imputed_traits.PhyloEM</a></code> </p>
+            <p><code><a href="imputed_traits.html">imputed_traits</a></code> </p>
           </td>
           <td><p>Ancestral State Reconstruction</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="model_selection.html">model_selection</a></code> <code><a href="model_selection.html">model_selection.PhyloEM</a></code> </p>
+            <p><code><a href="model_selection.html">model_selection</a></code> </p>
           </td>
           <td><p>Model Selection of a fitted object</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="residuals.PhyloEM.html">residuals.PhyloEM</a></code> </p>
+            <p><code><a href="residuals.PhyloEM.html">residuals</a></code> </p>
           </td>
           <td><p>Residuals of a fitted object</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="enlight.html">enlight</a></code> <code><a href="enlight.html">enlight.PhyloEM</a></code> </p>
+            <p><code><a href="enlight.html">enlight</a></code> </p>
           </td>
           <td><p>Make the result lighter</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="log_likelihood.html">log_likelihood</a></code> <code><a href="log_likelihood.html">log_likelihood.params_process</a></code> <code><a href="log_likelihood.html">log_likelihood.PhyloEM</a></code> </p>
+            <p><code><a href="log_likelihood.html">log_likelihood</a></code> </p>
           </td>
           <td><p>Log Likelihood of a fitted object</p></td>
         </tr>
@@ -176,7 +176,7 @@ <h2 id="section-parameters-and-simulations" class="hasAnchor"><a href="#section-
         <tr>
           <!--  -->
           <td>
-            <p><code><a href="simul_process.html">simul_process</a></code> <code><a href="simul_process.html">simul_process.params_process</a></code> <code><a href="simul_process.html">simul_process.PhyloEM</a></code> </p>
+            <p><code><a href="simul_process.html">simul_process</a></code> </p>
           </td>
           <td><p>Simulate a Stochastic Process on a tree</p></td>
         </tr><tr>
@@ -200,25 +200,25 @@ <h2 id="section-parameters-and-simulations" class="hasAnchor"><a href="#section-
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="params_process.character.html">params_process.character</a></code> </p>
+            <p><code><a href="params_process.character.html">params_process</a></code> </p>
           </td>
           <td><p>Create an object <code>params_process</code></p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="plot.params_process.html">plot.params_process</a></code> </p>
+            <p><code><a href="plot.params_process.html">plot</a></code> </p>
           </td>
           <td><p>Plot for class <code>simul_process</code></p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.simul_process.html">extract.simul_process</a></code> </p>
+            <p><code><a href="extract.simul_process.html">extract</a></code> </p>
           </td>
           <td><p>Extraction of simulated traits</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="log_likelihood.html">log_likelihood</a></code> <code><a href="log_likelihood.html">log_likelihood.params_process</a></code> <code><a href="log_likelihood.html">log_likelihood.PhyloEM</a></code> </p>
+            <p><code><a href="log_likelihood.html">log_likelihood</a></code> </p>
           </td>
           <td><p>Log Likelihood of a fitted object</p></td>
         </tr>
@@ -238,13 +238,13 @@ <h2 id="section-identifiability" class="hasAnchor"><a href="#section-identifiabi
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.equivalent_shifts.html">extract.equivalent_shifts</a></code> </p>
+            <p><code><a href="extract.equivalent_shifts.html">extract</a></code> </p>
           </td>
           <td><p>Extract the shifts values for one trait.</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="plot.equivalent_shifts.html">plot.equivalent_shifts</a></code> </p>
+            <p><code><a href="plot.equivalent_shifts.html">plot</a></code> </p>
           </td>
           <td><p>Plot all the equivalent solutions.</p></td>
         </tr>
@@ -265,13 +265,13 @@ <h2 id="section-parsimony-and-enumeration" class="hasAnchor"><a href="#section-p
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.enumerate_parsimony.html">extract.enumerate_parsimony</a></code> </p>
+            <p><code><a href="extract.enumerate_parsimony.html">extract</a></code> </p>
           </td>
           <td><p>Extract the result of <code>enumerate_parsimony</code> at a node.</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="plot.enumerate_parsimony.html">plot.enumerate_parsimony</a></code> </p>
+            <p><code><a href="plot.enumerate_parsimony.html">plot</a></code> </p>
           </td>
           <td><p>Plot all the equivalent solutions.</p></td>
         </tr><tr>
@@ -283,7 +283,7 @@ <h2 id="section-parsimony-and-enumeration" class="hasAnchor"><a href="#section-p
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.partitionsNumber.html">extract.partitionsNumber</a></code> </p>
+            <p><code><a href="extract.partitionsNumber.html">extract</a></code> </p>
           </td>
           <td><p>Extract from object <code>partitionsNumber</code></p></td>
         </tr><tr>
@@ -295,7 +295,7 @@ <h2 id="section-parsimony-and-enumeration" class="hasAnchor"><a href="#section-p
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.parsimonyNumber.html">extract.parsimonyNumber</a></code> </p>
+            <p><code><a href="extract.parsimonyNumber.html">extract</a></code> </p>
           </td>
           <td><p>Extraction of the actual number of solutions.</p></td>
         </tr><tr>
@@ -307,7 +307,7 @@ <h2 id="section-parsimony-and-enumeration" class="hasAnchor"><a href="#section-p
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="extract.parsimonyCost.html">extract.parsimonyCost</a></code> </p>
+            <p><code><a href="extract.parsimonyCost.html">extract</a></code> </p>
           </td>
           <td><p>Extraction of the actual number of solutions.</p></td>
         </tr>
diff --git a/docs/reference/init.EM.lasso.html b/docs/reference/init.EM.lasso.html
index 26bbc6a..cbc036d 100644
--- a/docs/reference/init.EM.lasso.html
+++ b/docs/reference/init.EM.lasso.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -89,7 +89,7 @@ <h1>Initialisation of the shifts using Lasso.</h1>
 <code>incidence.matrix</code> and <code>shifts.list_to_vector</code> for further details).</p>
     
 
-    <pre><span class='fu'>init.EM.lasso</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>Y_data_imp</span> <span class='kw'>=</span> <span class='no'>Y_data</span>,
+    <pre class="usage"><span class='fu'>init.EM.lasso</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='kw'>Y_data_imp</span> <span class='kw'>=</span> <span class='no'>Y_data</span>,
   <span class='kw'>Y_data_vec_known</span> <span class='kw'>=</span> <span class='fu'>as.vector</span>(<span class='no'>Y_data</span>), <span class='no'>process</span>,
   <span class='kw'>times_shared</span> <span class='kw'>=</span> <span class='fu'><a href='compute_times_ca.html'>compute_times_ca</a></span>(<span class='no'>phylo</span>), <span class='no'>distances_phylo</span>, <span class='no'>nbr_of_shifts</span>,
   <span class='kw'>K_lag_init</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>use_sigma</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params_sigma</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
diff --git a/docs/reference/init.allocate_regimes_from_shifts.html b/docs/reference/init.allocate_regimes_from_shifts.html
index 80a5fe7..62bc405 100644
--- a/docs/reference/init.allocate_regimes_from_shifts.html
+++ b/docs/reference/init.allocate_regimes_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initialisation for the allocation of shifts.</h1>
 at nodes and tips, with the regime (0) at the root.</p>
     
 
-    <pre><span class='fu'>init.allocate_regimes_from_shifts</span>(<span class='no'>phy</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>init.allocate_regimes_from_shifts</span>(<span class='no'>phy</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.alpha.gamma.estimation.html b/docs/reference/init.alpha.gamma.estimation.html
index f42385e..7e268b9 100644
--- a/docs/reference/init.alpha.gamma.estimation.html
+++ b/docs/reference/init.alpha.gamma.estimation.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Initialisation the selection strength alpha using robust estimation</h1>
 (function <code>init.EM.lasso</code>).</p>
     
 
-    <pre><span class='fu'>init.alpha.gamma.estimation</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>nbr_of_shifts</span>, <span class='no'>times_shared</span>,
+    <pre class="usage"><span class='fu'>init.alpha.gamma.estimation</span>(<span class='no'>phylo</span>, <span class='no'>Y_data</span>, <span class='no'>nbr_of_shifts</span>, <span class='no'>times_shared</span>,
   <span class='no'>distances_phylo</span>, <span class='no'>T_tree</span>, <span class='no'>subtree.list</span>, <span class='no'>max_triplet_number</span>, <span class='no'>alpha_known</span>,
   <span class='no'>method.init.alpha.estimation</span>, <span class='no'>tol</span>, <span class='no'>h_tree</span>, <span class='no'>miss</span>, <span class='no'>masque_data</span>, <span class='no'>independent</span>,
   <span class='no'>...</span>)</pre>
diff --git a/docs/reference/init.compute_betas_from_shifts.html b/docs/reference/init.compute_betas_from_shifts.html
index e84d595..0b0b99d 100644
--- a/docs/reference/init.compute_betas_from_shifts.html
+++ b/docs/reference/init.compute_betas_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initialisation for the computation of the optimal values</h1>
 tips, with the value at the root.</p>
     
 
-    <pre><span class='fu'>init.compute_betas_from_shifts</span>(<span class='no'>phy</span>, <span class='no'>optimal.value</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>init.compute_betas_from_shifts</span>(<span class='no'>phy</span>, <span class='no'>optimal.value</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.enumerate_parsimony.html b/docs/reference/init.enumerate_parsimony.html
index d3cc902..6192905 100644
--- a/docs/reference/init.enumerate_parsimony.html
+++ b/docs/reference/init.enumerate_parsimony.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initialization for the enumeration of parsimonious solutions.</h1>
 and initialize the correct data structure.</p>
     
 
-    <pre><span class='fu'>init.enumerate_parsimony</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>, <span class='no'>pos</span>)</pre>
+    <pre class="usage"><span class='fu'>init.enumerate_parsimony</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>, <span class='no'>pos</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.incidence.matrix.full.html b/docs/reference/init.incidence.matrix.full.html
index 29fbb99..8a5c03c 100644
--- a/docs/reference/init.incidence.matrix.full.html
+++ b/docs/reference/init.incidence.matrix.full.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Initialization for incidence matrix (full tree)</h1>
  matrix of the full tree in <code>incidence.matrix.full</code>.</p>
     
 
-    <pre><span class='fu'>init.incidence.matrix.full</span>(<span class='no'>phy</span>)</pre>
+    <pre class="usage"><span class='fu'>init.incidence.matrix.full</span>(<span class='no'>phy</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.incidence.matrix.html b/docs/reference/init.incidence.matrix.html
index 837eb82..bd3f956 100644
--- a/docs/reference/init.incidence.matrix.html
+++ b/docs/reference/init.incidence.matrix.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Initialization for incidence matrix</h1>
 in <code>incidence.matrix</code>.</p>
     
 
-    <pre><span class='fu'>init.incidence.matrix</span>(<span class='no'>phy</span>)</pre>
+    <pre class="usage"><span class='fu'>init.incidence.matrix</span>(<span class='no'>phy</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.parsimonyCost.html b/docs/reference/init.parsimonyCost.html
index ba2edd2..2cafaf9 100644
--- a/docs/reference/init.parsimonyCost.html
+++ b/docs/reference/init.parsimonyCost.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initialization for parsimonyCost.</h1>
 NAs everywhere, except for the tips.</p>
     
 
-    <pre><span class='fu'>init.parsimonyCost</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>)</pre>
+    <pre class="usage"><span class='fu'>init.parsimonyCost</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.parsimonyNumber.html b/docs/reference/init.parsimonyNumber.html
index 252a003..eeddf33 100644
--- a/docs/reference/init.parsimonyNumber.html
+++ b/docs/reference/init.parsimonyNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Initialization for parsimonyNumber.</h1>
 NAs everywhere, except for the tips.</p>
     
 
-    <pre><span class='fu'>init.parsimonyNumber</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>)</pre>
+    <pre class="usage"><span class='fu'>init.parsimonyNumber</span>(<span class='no'>phy</span>, <span class='no'>clusters</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.simulate.BM.html b/docs/reference/init.simulate.BM.html
index 485124a..76da325 100644
--- a/docs/reference/init.simulate.BM.html
+++ b/docs/reference/init.simulate.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Initialize BM</h1>
     <p>Function used in <code>simulate</code> for BM initialisation.</p>
     
 
-    <pre><span class='fu'>init.simulate.BM</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>simulate_random</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>init.simulate.BM</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>simulate_random</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.simulate.OU.html b/docs/reference/init.simulate.OU.html
index 626b4f6..9adcdfd 100644
--- a/docs/reference/init.simulate.OU.html
+++ b/docs/reference/init.simulate.OU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Initialize state and expectation matrices</h1>
     <p>Function used in <code>simulate</code> for OU initialisation.</p>
     
 
-    <pre><span class='fu'>init.simulate.OU</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>optimal.value</span>, <span class='no'>simulate_random</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>init.simulate.OU</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>optimal.value</span>, <span class='no'>simulate_random</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/init.simulate.StateAndExp.html b/docs/reference/init.simulate.StateAndExp.html
index 3aa2357..1618830 100644
--- a/docs/reference/init.simulate.StateAndExp.html
+++ b/docs/reference/init.simulate.StateAndExp.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Initialize state and expectation matrices</h1>
     <p>Function used in <code>simulate</code> for BM/OU initialisations.</p>
     
 
-    <pre><span class='fu'>init.simulate.StateAndExp</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>simulate_random</span>)</pre>
+    <pre class="usage"><span class='fu'>init.simulate.StateAndExp</span>(<span class='no'>phy</span>, <span class='no'>p</span>, <span class='no'>root.state</span>, <span class='no'>simulate_random</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/is.in.ranges.html b/docs/reference/is.in.ranges.html
index 10e9e29..0d6d7e0 100644
--- a/docs/reference/is.in.ranges.html
+++ b/docs/reference/is.in.ranges.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Check wether parameters are in ranges.</h1>
 in the defined ranges.</p>
     
 
-    <pre><span class='fu'>is.in.ranges</span>(<span class='no'>p</span>, <span class='no'>min</span>, <span class='no'>max</span>)</pre>
+    <pre class="usage"><span class='fu'>is.in.ranges</span>(<span class='no'>p</span>, <span class='no'>min</span>, <span class='no'>max</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html b/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html
index b75dbd8..dd52830 100644
--- a/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html
+++ b/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -88,7 +88,7 @@ <h1>Do a lasso regression with the number of non-zero variables fixed.</h1>
 <code>init.EM.lasso</code>, <code>segmentation.OU.specialCase.lasso</code>, ...</p>
     
 
-    <pre><span class='fu'>lasso_regression_K_fixed.glmnet_multivariate</span>(<span class='no'>Yp</span>, <span class='no'>Xp</span>, <span class='no'>K</span>, <span class='kw'>root</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+    <pre class="usage"><span class='fu'>lasso_regression_K_fixed.glmnet_multivariate</span>(<span class='no'>Yp</span>, <span class='no'>Xp</span>, <span class='no'>K</span>, <span class='kw'>root</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>penscale</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>ncol</span>(<span class='no'>Xp</span>)), <span class='kw'>K_lag</span> <span class='kw'>=</span> <span class='fl'>0</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/log_likelihood.html b/docs/reference/log_likelihood.html
index ebb5f07..3aff4a6 100644
--- a/docs/reference/log_likelihood.html
+++ b/docs/reference/log_likelihood.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Log Likelihood of a fitted object</h1>
     <p><code>log_likelihood</code> computes the log likelihood of some parameters.</p>
     
 
-    <pre><span class='fu'>log_likelihood</span>(<span class='no'>x</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>log_likelihood</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for params_process</span>
 <span class='fu'>log_likelihood</span>(<span class='no'>x</span>, <span class='no'>Y_data</span>, <span class='no'>phylo</span>, <span class='no'>...</span>)
diff --git a/docs/reference/matrix_of_possibles.html b/docs/reference/matrix_of_possibles.html
index 78b471e..6e1c153 100644
--- a/docs/reference/matrix_of_possibles.html
+++ b/docs/reference/matrix_of_possibles.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Compute parent matrix from possibles daughter matrices.</h1>
 the node (a group for the parent being fixed).</p>
     
 
-    <pre><span class='fu'>matrix_of_possibles</span>(<span class='no'>matrices</span>)</pre>
+    <pre class="usage"><span class='fu'>matrix_of_possibles</span>(<span class='no'>matrices</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/merge_complementary_vectors.html b/docs/reference/merge_complementary_vectors.html
index 7deb896..fb7706a 100644
--- a/docs/reference/merge_complementary_vectors.html
+++ b/docs/reference/merge_complementary_vectors.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Merge several complementary vectors into one.</h1>
 for each entry), and merge them into one.</p>
     
 
-    <pre><span class='fu'>merge_complementary_vectors</span>(<span class='no'>comb</span>, <span class='no'>mat</span>)</pre>
+    <pre class="usage"><span class='fu'>merge_complementary_vectors</span>(<span class='no'>comb</span>, <span class='no'>mat</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/merge_params_independent.html b/docs/reference/merge_params_independent.html
index 439ab0c..580f660 100644
--- a/docs/reference/merge_params_independent.html
+++ b/docs/reference/merge_params_independent.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Merge a list of independent parameters into into one parameter</h1>
 The reverse operation is done by <code>split_params_independent</code></p>
     
 
-    <pre><span class='fu'>merge_params_independent</span>(<span class='no'>params_split</span>)</pre>
+    <pre class="usage"><span class='fu'>merge_params_independent</span>(<span class='no'>params_split</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/model_selection.html b/docs/reference/model_selection.html
index 63abac2..b05be75 100644
--- a/docs/reference/model_selection.html
+++ b/docs/reference/model_selection.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Model Selection of a fitted object</h1>
 object, and returns the same fitted object.</p>
     
 
-    <pre><span class='fu'>model_selection</span>(<span class='no'>x</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>model_selection</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for PhyloEM</span>
 <span class='fu'>model_selection</span>(<span class='no'>x</span>, <span class='kw'>method.selection</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"LINselect"</span>, <span class='st'>"DDSE"</span>,
diff --git a/docs/reference/monkeys.html b/docs/reference/monkeys.html
index ac96ad7..9767049 100644
--- a/docs/reference/monkeys.html
+++ b/docs/reference/monkeys.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>New World Monkeys dataset</h1>
 New World monkeys (platyrrhine).</p>
     
 
-    <pre><span class='no'>monkeys</span></pre>
+    <pre class="usage"><span class='no'>monkeys</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
diff --git a/docs/reference/optimize_costs_given_shift_position.OU.specialCase.html b/docs/reference/optimize_costs_given_shift_position.OU.specialCase.html
index 72af6ab..99386f7 100644
--- a/docs/reference/optimize_costs_given_shift_position.OU.specialCase.html
+++ b/docs/reference/optimize_costs_given_shift_position.OU.specialCase.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Minimization of the sum of costs, given the shift position.</h1>
 costs when the shift position is fixed.</p>
     
 
-    <pre><span class='fu'>optimize_costs_given_shift_position.OU.specialCase</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>,
+    <pre class="usage"><span class='fu'>optimize_costs_given_shift_position.OU.specialCase</span>(<span class='no'>phylo</span>, <span class='no'>conditional_law_X</span>,
   <span class='no'>selection.strength</span>, <span class='no'>shifts_edges</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/params_BM.html b/docs/reference/params_BM.html
index 45336f1..42b876f 100644
--- a/docs/reference/params_BM.html
+++ b/docs/reference/params_BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Create an object <code>params_process</code> for a BM</h1>
 default values.</p>
     
 
-    <pre><span class='fu'>params_BM</span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>variance</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>), <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+    <pre class="usage"><span class='fu'>params_BM</span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>variance</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>), <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>value.root</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>0</span>, <span class='no'>p</span>), <span class='kw'>exp.root</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>0</span>, <span class='no'>p</span>), <span class='kw'>var.root</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>),
   <span class='kw'>edges</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>matrix</span>(<span class='fl'>0</span>, <span class='no'>p</span>, <span class='fu'>length</span>(<span class='no'>edges</span>)),
   <span class='kw'>relativeTimes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nbr_of_shifts</span> <span class='kw'>=</span> <span class='fu'>length</span>(<span class='no'>edges</span>), <span class='kw'>phylo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
diff --git a/docs/reference/params_OU.html b/docs/reference/params_OU.html
index 57399cf..10f353f 100644
--- a/docs/reference/params_OU.html
+++ b/docs/reference/params_OU.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Create an object <code>params_process</code> for an OU</h1>
 default values.</p>
     
 
-    <pre><span class='fu'>params_OU</span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>variance</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>), <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>,
+    <pre class="usage"><span class='fu'>params_OU</span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>variance</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>), <span class='kw'>selection.strength</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>,
   <span class='no'>p</span>), <span class='kw'>optimal.value</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>0</span>, <span class='no'>p</span>), <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>stationary.root</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>value.root</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>0</span>, <span class='no'>p</span>), <span class='kw'>exp.root</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>0</span>, <span class='no'>p</span>), <span class='kw'>var.root</span> <span class='kw'>=</span> <span class='fu'>diag</span>(<span class='fl'>1</span>, <span class='no'>p</span>, <span class='no'>p</span>),
   <span class='kw'>edges</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>matrix</span>(<span class='fl'>0</span>, <span class='no'>p</span>, <span class='fu'>length</span>(<span class='no'>edges</span>)),
diff --git a/docs/reference/params_process.PhyloEM.html b/docs/reference/params_process.PhyloEM.html
index 0cb7264..ecd0ded 100644
--- a/docs/reference/params_process.PhyloEM.html
+++ b/docs/reference/params_process.PhyloEM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Parameter estimates</h1>
 infered parameters of the process.</p>
     
 
-    <pre><span class='co'># S3 method for PhyloEM</span>
+    <pre class="usage"><span class='co'># S3 method for PhyloEM</span>
 <span class='fu'><a href='params_process.html'>params_process</a></span>(<span class='no'>x</span>, <span class='kw'>method.selection</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>K</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>rBM</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>init</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/params_process.character.html b/docs/reference/params_process.character.html
index 6c9025e..0cf7e1d 100644
--- a/docs/reference/params_process.character.html
+++ b/docs/reference/params_process.character.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Create an object <code>params_process</code></h1>
 provided values of the paramerters.</p>
     
 
-    <pre><span class='co'># S3 method for character</span>
+    <pre class="usage"><span class='co'># S3 method for character</span>
 <span class='fu'><a href='params_process.html'>params_process</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/params_process.html b/docs/reference/params_process.html
index 76ffe78..8da85c2 100644
--- a/docs/reference/params_process.html
+++ b/docs/reference/params_process.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Create an object params_process</h1>
 <code>params_process</code>.</p>
     
 
-    <pre><span class='fu'>params_process</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>params_process</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/parsimonyCost-2.png b/docs/reference/parsimonyCost-2.png
index 4e063ac..5e22cd7 100644
Binary files a/docs/reference/parsimonyCost-2.png and b/docs/reference/parsimonyCost-2.png differ
diff --git a/docs/reference/parsimonyCost.html b/docs/reference/parsimonyCost.html
index 03e8752..901e398 100644
--- a/docs/reference/parsimonyCost.html
+++ b/docs/reference/parsimonyCost.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -87,7 +87,7 @@ <h1>Minimal number of shifts needed to get a clustering.</h1>
 tips.</p>
     
 
-    <pre><span class='fu'>parsimonyCost</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
+    <pre class="usage"><span class='fu'>parsimonyCost</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/parsimonyNumber-2.png b/docs/reference/parsimonyNumber-2.png
index 5fd242e..878c240 100644
Binary files a/docs/reference/parsimonyNumber-2.png and b/docs/reference/parsimonyNumber-2.png differ
diff --git a/docs/reference/parsimonyNumber.html b/docs/reference/parsimonyNumber.html
index 8db867a..159a7ed 100644
--- a/docs/reference/parsimonyNumber.html
+++ b/docs/reference/parsimonyNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Number of equivalent parsimonious allocations.</h1>
 with a given clustering of the tips.</p>
     
 
-    <pre><span class='fu'>parsimonyNumber</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
+    <pre class="usage"><span class='fu'>parsimonyNumber</span>(<span class='no'>phylo</span>, <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, <span class='fu'>length</span>(<span class='no'>phylo</span>$<span class='no'>tip.label</span>)))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/partitionsNumber-2.png b/docs/reference/partitionsNumber-2.png
index 6934353..f4eaa06 100644
Binary files a/docs/reference/partitionsNumber-2.png and b/docs/reference/partitionsNumber-2.png differ
diff --git a/docs/reference/partitionsNumber.html b/docs/reference/partitionsNumber.html
index 42656ee..83610e1 100644
--- a/docs/reference/partitionsNumber.html
+++ b/docs/reference/partitionsNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Number of different models</h1>
 tree in npart = K + 1 colors.</p>
     
 
-    <pre><span class='fu'>partitionsNumber</span>(<span class='no'>phylo</span>, <span class='no'>npart</span>)</pre>
+    <pre class="usage"><span class='fu'>partitionsNumber</span>(<span class='no'>phylo</span>, <span class='no'>npart</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/penalty_BaraudGiraudHuet_likelihood.html b/docs/reference/penalty_BaraudGiraudHuet_likelihood.html
index 6e5112e..c14b8f3 100644
--- a/docs/reference/penalty_BaraudGiraudHuet_likelihood.html
+++ b/docs/reference/penalty_BaraudGiraudHuet_likelihood.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -87,7 +87,7 @@ <h1>Penalty function type Baraud Giraud Huet.</h1>
 such that sum(exp(-Delta_K)) &lt; infty.</p>
     
 
-    <pre><span class='fu'>penalty_BaraudGiraudHuet_likelihood</span>(<span class='no'>K</span>, <span class='no'>model_complexity</span>, <span class='no'>ntaxa</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='fl'>1.1</span>)</pre>
+    <pre class="usage"><span class='fu'>penalty_BaraudGiraudHuet_likelihood</span>(<span class='no'>K</span>, <span class='no'>model_complexity</span>, <span class='no'>ntaxa</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='fl'>1.1</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/penalty_BirgeMassart_shape1.html b/docs/reference/penalty_BirgeMassart_shape1.html
index 84b0715..e53526d 100644
--- a/docs/reference/penalty_BirgeMassart_shape1.html
+++ b/docs/reference/penalty_BirgeMassart_shape1.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Penalty function type Birgé-Massart 1</h1>
 L_K = B + 1/K * log(model_complexity).</p>
     
 
-    <pre><span class='fu'>penalty_BirgeMassart_shape1</span>(<span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>model_complexity</span>, <span class='kw'>B</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
+    <pre class="usage"><span class='fu'>penalty_BirgeMassart_shape1</span>(<span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>model_complexity</span>, <span class='kw'>B</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/penalty_BirgeMassart_shape2.html b/docs/reference/penalty_BirgeMassart_shape2.html
index 2606805..0d90ab4 100644
--- a/docs/reference/penalty_BirgeMassart_shape2.html
+++ b/docs/reference/penalty_BirgeMassart_shape2.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Penalty function type Birgé-Massart 2</h1>
 It dominates the penalty defined by <code>penalty_BirgeMassart_shape1</code>.</p>
     
 
-    <pre><span class='fu'>penalty_BirgeMassart_shape2</span>(<span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>model_complexity</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='fl'>2.5</span>)</pre>
+    <pre class="usage"><span class='fu'>penalty_BirgeMassart_shape2</span>(<span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>model_complexity</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='fl'>2.5</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/penalty_pBIC.html b/docs/reference/penalty_pBIC.html
index f5865f7..5a3d98f 100644
--- a/docs/reference/penalty_pBIC.html
+++ b/docs/reference/penalty_pBIC.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Penalty function type pBIC</h1>
     <p><code>penalty_pBIC_scalarOU</code> is the pBIC.</p>
     
 
-    <pre><span class='fu'>penalty_pBIC</span>(<span class='no'>all_params</span>, <span class='no'>model_complexity</span>, <span class='no'>independent</span>, <span class='no'>tree</span>, <span class='no'>times_shared</span>,
+    <pre class="usage"><span class='fu'>penalty_pBIC</span>(<span class='no'>all_params</span>, <span class='no'>model_complexity</span>, <span class='no'>independent</span>, <span class='no'>tree</span>, <span class='no'>times_shared</span>,
   <span class='no'>distances_phylo</span>, <span class='no'>T_tree</span>, <span class='no'>p</span>, <span class='no'>K</span>, <span class='no'>ntaxa</span>, <span class='no'>process</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/plot.PhyloEM.html b/docs/reference/plot.PhyloEM.html
index 7c1d262..e5504d8 100644
--- a/docs/reference/plot.PhyloEM.html
+++ b/docs/reference/plot.PhyloEM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Plot for class <code>PhyloEM</code></h1>
 <code><a href='PhyloEM.html'>PhyloEM</a></code>, and plots the result of the inferrence.</p>
     
 
-    <pre><span class='co'># S3 method for PhyloEM</span>
+    <pre class="usage"><span class='co'># S3 method for PhyloEM</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>traits</span> <span class='kw'>=</span> <span class='fl'>1</span>:(<span class='no'>x</span>$<span class='no'>p</span>), <span class='kw'>params</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>method.selection</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>automatic_colors</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>color_characters</span> <span class='kw'>=</span> <span class='st'>"black"</span>, <span class='kw'>color_edges</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
@@ -93,8 +93,9 @@ <h1>Plot for class <code>PhyloEM</code></h1>
   <span class='kw'>shifts_cex</span> <span class='kw'>=</span> <span class='fl'>0.6</span>, <span class='kw'>shifts_bg</span> <span class='kw'>=</span> <span class='st'>"chocolate4"</span>, <span class='kw'>root_bg</span> <span class='kw'>=</span> <span class='st'>"chocolate4"</span>,
   <span class='kw'>shifts_adj</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>root_adj</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>color_shifts_regimes</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>regime_boxes</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>alpha_border</span> <span class='kw'>=</span> <span class='fl'>70</span>, <span class='kw'>show.tip.label</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>label_cex</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>label_offset</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>axis_cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>edge.width</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-  <span class='kw'>margin_plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>gray_scale</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>root.edge</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+  <span class='kw'>label_cex</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>label_font</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>label_offset</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>axis_cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+  <span class='kw'>axis_las</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>edge.width</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>margin_plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>gray_scale</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>root.edge</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
@@ -221,6 +222,10 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Ar
       <td><p>if <code>show.tip.label=TRUE</code>, the size of the labels. Default
 to 0.5.</p></td>
     </tr>
+    <tr>
+      <th>label_font</th>
+      <td><p>if <code>show.tip.label=TRUE</code>, the font of the labels (see par).</p></td>
+    </tr>
     <tr>
       <th>label_offset</th>
       <td><p>if <code>show.tip.label=TRUE</code>, the size of the offset between
@@ -230,6 +235,10 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Ar
       <th>axis_cex</th>
       <td><p>cex for the label values of the plot. Default to 0.7.</p></td>
     </tr>
+    <tr>
+      <th>axis_las</th>
+      <td><p>las for the label values of the plot. Default to 0 (see par).</p></td>
+    </tr>
     <tr>
       <th>edge.width</th>
       <td><p>width of the edge. Default to 1.</p></td>
diff --git a/docs/reference/plot.enumerate_parsimony.html b/docs/reference/plot.enumerate_parsimony.html
index b119529..3aa0230 100644
--- a/docs/reference/plot.enumerate_parsimony.html
+++ b/docs/reference/plot.enumerate_parsimony.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Plot all the equivalent solutions.</h1>
 solutions.</p>
     
 
-    <pre><span class='co'># S3 method for enumerate_parsimony</span>
+    <pre class="usage"><span class='co'># S3 method for enumerate_parsimony</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>numbering</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>nbr_col</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/plot.equivalent_shifts.html b/docs/reference/plot.equivalent_shifts.html
index e1db43e..e6889f4 100644
--- a/docs/reference/plot.equivalent_shifts.html
+++ b/docs/reference/plot.equivalent_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Plot all the equivalent solutions.</h1>
 and a coloration of the branches in term of regimes.</p>
     
 
-    <pre><span class='co'># S3 method for equivalent_shifts</span>
+    <pre class="usage"><span class='co'># S3 method for equivalent_shifts</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>numbering</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>colors_tips</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nbr_col</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>gray_scale</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
     
diff --git a/docs/reference/plot.params_process.html b/docs/reference/plot.params_process.html
index 71e3bae..40983ab 100644
--- a/docs/reference/plot.params_process.html
+++ b/docs/reference/plot.params_process.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Plot for class <code>simul_process</code></h1>
 with some data at the tips of the tree.</p>
     
 
-    <pre><span class='co'># S3 method for params_process</span>
+    <pre class="usage"><span class='co'># S3 method for params_process</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='no'>phylo</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>traits</span>,
   <span class='kw'>automatic_colors</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>color_characters</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
   <span class='kw'>color_edges</span> <span class='kw'>=</span> <span class='st'>"black"</span>, <span class='kw'>plot_ancestral_states</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
diff --git a/docs/reference/prod.index.html b/docs/reference/prod.index.html
index 07a8a77..42d411b 100644
--- a/docs/reference/prod.index.html
+++ b/docs/reference/prod.index.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Product of elements of a matrix</h1>
     <p><code>prod.index</code> return the procuct of choosen elements of a matrix.</p>
     
 
-    <pre><span class='co'># S3 method for index</span>
+    <pre class="usage"><span class='co'># S3 method for index</span>
 <span class='fu'>prod</span>(<span class='no'>X</span>, <span class='no'>Id</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/qr.solve_exact.html b/docs/reference/qr.solve_exact.html
index 7405522..1891ff0 100644
--- a/docs/reference/qr.solve_exact.html
+++ b/docs/reference/qr.solve_exact.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>exact qr.solve</h1>
 of <code>qr.solve</code>).</p>
     
 
-    <pre><span class='fu'>qr.solve_exact</span>(<span class='no'>a</span>, <span class='no'>b</span>, <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>1e-07</span>)</pre>
+    <pre class="usage"><span class='fu'>qr.solve_exact</span>(<span class='no'>a</span>, <span class='no'>b</span>, <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>1e-07</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/recursionDown.html b/docs/reference/recursionDown.html
index 9132ad5..b3c108e 100644
--- a/docs/reference/recursionDown.html
+++ b/docs/reference/recursionDown.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Generic recursion down the tree.</h1>
 daughters rows of matrix param.</p>
     
 
-    <pre><span class='fu'>recursionDown</span>(<span class='no'>phy</span>, <span class='no'>params</span>, <span class='no'>updateDown</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>recursionDown</span>(<span class='no'>phy</span>, <span class='no'>params</span>, <span class='no'>updateDown</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/residuals.PhyloEM.html b/docs/reference/residuals.PhyloEM.html
index 1e70ae3..0d26db7 100644
--- a/docs/reference/residuals.PhyloEM.html
+++ b/docs/reference/residuals.PhyloEM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Residuals of a fitted object</h1>
     <p><code>residuals</code> computes the residuals of some parameters.</p>
     
 
-    <pre><span class='co'># S3 method for PhyloEM</span>
+    <pre class="usage"><span class='co'># S3 method for PhyloEM</span>
 <span class='fu'>residuals</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/sample_edges_intervals.html b/docs/reference/sample_edges_intervals.html
index 6b9db0b..0d518dc 100644
--- a/docs/reference/sample_edges_intervals.html
+++ b/docs/reference/sample_edges_intervals.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Sample equally espaced edges.</h1>
 regularly espaced on the height of the tree.</p>
     
 
-    <pre><span class='fu'>sample_edges_intervals</span>(<span class='no'>tree</span>, <span class='no'>K</span>)</pre>
+    <pre class="usage"><span class='fu'>sample_edges_intervals</span>(<span class='no'>tree</span>, <span class='no'>K</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/sample_shifts_edges.html b/docs/reference/sample_shifts_edges.html
index 85e988d..ec5a71e 100644
--- a/docs/reference/sample_shifts_edges.html
+++ b/docs/reference/sample_shifts_edges.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Sample shifts edges in a parsimonious way.</h1>
 <code>sample_edges_intervals</code>.</p>
     
 
-    <pre><span class='fu'>sample_shifts_edges</span>(<span class='no'>tree</span>, <span class='no'>K</span>, <span class='kw'>part.list</span> <span class='kw'>=</span> <span class='fu'><a href='enumerate_tips_under_edges.html'>enumerate_tips_under_edges</a></span>(<span class='no'>tree</span>))</pre>
+    <pre class="usage"><span class='fu'>sample_shifts_edges</span>(<span class='no'>tree</span>, <span class='no'>K</span>, <span class='kw'>part.list</span> <span class='kw'>=</span> <span class='fu'><a href='enumerate_tips_under_edges.html'>enumerate_tips_under_edges</a></span>(<span class='no'>tree</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/scale_params.html b/docs/reference/scale_params.html
index f0c4116..cbcff84 100644
--- a/docs/reference/scale_params.html
+++ b/docs/reference/scale_params.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Scale variance and selection strenght from a linear transform</h1>
     <p>Used for process equivalencies on re-scaled trees.</p>
     
 
-    <pre><span class='fu'>scale_params</span>(<span class='no'>params</span>, <span class='no'>f</span>)</pre>
+    <pre class="usage"><span class='fu'>scale_params</span>(<span class='no'>params</span>, <span class='no'>f</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/segmentation.BM.html b/docs/reference/segmentation.BM.html
index 4b119d0..282bf5e 100644
--- a/docs/reference/segmentation.BM.html
+++ b/docs/reference/segmentation.BM.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Segmentation in the BM case</h1>
     <p><code>segmentation.BM</code> performs the segmentation algorithm described.</p>
     
 
-    <pre><span class='fu'>segmentation.BM</span>(<span class='no'>nbr_of_shifts</span>, <span class='no'>costs0</span>, <span class='no'>diff_exp</span>)</pre>
+    <pre class="usage"><span class='fu'>segmentation.BM</span>(<span class='no'>nbr_of_shifts</span>, <span class='no'>costs0</span>, <span class='no'>diff_exp</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/segmentation.OU.specialCase.lasso.html b/docs/reference/segmentation.OU.specialCase.lasso.html
index beec15a..f3653c4 100644
--- a/docs/reference/segmentation.OU.specialCase.lasso.html
+++ b/docs/reference/segmentation.OU.specialCase.lasso.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Segmentation in the OU special case, using lasso regression</h1>
 lasso regression to select for the edges where the shifts are added.</p>
     
 
-    <pre><span class='fu'>segmentation.OU.specialCase.lasso</span>(<span class='no'>phylo</span>, <span class='no'>nbr_of_shifts</span>, <span class='no'>D</span>, <span class='no'>Xp</span>,
+    <pre class="usage"><span class='fu'>segmentation.OU.specialCase.lasso</span>(<span class='no'>phylo</span>, <span class='no'>nbr_of_shifts</span>, <span class='no'>D</span>, <span class='no'>Xp</span>,
   <span class='kw'>penscale</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>1</span>, (<span class='fu'>nrow</span>(<span class='no'>phylo</span>$<span class='no'>edge</span>) + <span class='fl'>1</span>)), <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/segmentation.OU.specialCase.same_shifts.html b/docs/reference/segmentation.OU.specialCase.same_shifts.html
index 46cb8aa..7d6e7ed 100644
--- a/docs/reference/segmentation.OU.specialCase.same_shifts.html
+++ b/docs/reference/segmentation.OU.specialCase.same_shifts.html
@@ -26,7 +26,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -87,7 +87,7 @@ <h1>Segmentation in the OU special case, conserving the same shifts
 <code>optimize_costs_given_shift_position.OU.specialCase</code>.</p>
     
 
-    <pre><span class='fu'>segmentation.OU.specialCase.same_shifts</span>(<span class='no'>phylo</span>, <span class='no'>shifts_old</span>, <span class='no'>D</span>, <span class='no'>Xp</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>segmentation.OU.specialCase.same_shifts</span>(<span class='no'>phylo</span>, <span class='no'>shifts_old</span>, <span class='no'>D</span>, <span class='no'>Xp</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/shifts.list_to_matrix.html b/docs/reference/shifts.list_to_matrix.html
index 2759107..f6c9ff8 100644
--- a/docs/reference/shifts.list_to_matrix.html
+++ b/docs/reference/shifts.list_to_matrix.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Compute the matrix of shifts.</h1>
 the lth line has the value of the shift on character l occuring on that branch b</p>
     
 
-    <pre><span class='fu'>shifts.list_to_matrix</span>(<span class='no'>phy</span>, <span class='no'>shifts</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>nrow</span>(<span class='no'>shifts</span>$<span class='no'>values</span>))</pre>
+    <pre class="usage"><span class='fu'>shifts.list_to_matrix</span>(<span class='no'>phy</span>, <span class='no'>shifts</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>nrow</span>(<span class='no'>shifts</span>$<span class='no'>values</span>))</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/shifts.list_to_vector.html b/docs/reference/shifts.list_to_vector.html
index dbf1591..6e6f318 100644
--- a/docs/reference/shifts.list_to_vector.html
+++ b/docs/reference/shifts.list_to_vector.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Compute the vector of shifts.</h1>
 the vector has the value of the shift occuring on that branch b.</p>
     
 
-    <pre><span class='fu'>shifts.list_to_vector</span>(<span class='no'>phy</span>, <span class='no'>shifts</span>)</pre>
+    <pre class="usage"><span class='fu'>shifts.list_to_vector</span>(<span class='no'>phy</span>, <span class='no'>shifts</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/shifts.matrix_to_list.html b/docs/reference/shifts.matrix_to_list.html
index c2f1d91..3fa4d2a 100644
--- a/docs/reference/shifts.matrix_to_list.html
+++ b/docs/reference/shifts.matrix_to_list.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute the list of shifts.</h1>
 to create the list description of the shifts.</p>
     
 
-    <pre><span class='fu'>shifts.matrix_to_list</span>(<span class='no'>delta</span>)</pre>
+    <pre class="usage"><span class='fu'>shifts.matrix_to_list</span>(<span class='no'>delta</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/shifts.vector_to_list.html b/docs/reference/shifts.vector_to_list.html
index c4dffe6..60406db 100644
--- a/docs/reference/shifts.vector_to_list.html
+++ b/docs/reference/shifts.vector_to_list.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Compute the list of shifts.</h1>
 to create the list description of the shifts.</p>
     
 
-    <pre><span class='fu'>shifts.vector_to_list</span>(<span class='no'>delta</span>)</pre>
+    <pre class="usage"><span class='fu'>shifts.vector_to_list</span>(<span class='no'>delta</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/shifts_to_simmap.html b/docs/reference/shifts_to_simmap.html
index 2557764..0dff541 100644
--- a/docs/reference/shifts_to_simmap.html
+++ b/docs/reference/shifts_to_simmap.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Simmap format mapping from list of edges</h1>
 simmap formated tree, mapped with corresponding regimes.</p>
     
 
-    <pre><span class='fu'>shifts_to_simmap</span>(<span class='no'>tree</span>, <span class='no'>shifts_edges</span>)</pre>
+    <pre class="usage"><span class='fu'>shifts_to_simmap</span>(<span class='no'>tree</span>, <span class='no'>shifts_edges</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/simul_process.html b/docs/reference/simul_process.html
index e62f303..1fc37f1 100644
--- a/docs/reference/simul_process.html
+++ b/docs/reference/simul_process.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Simulate a Stochastic Process on a tree</h1>
     <p><code>simulate</code> simulate a stochastic process on a tree.</p>
     
 
-    <pre><span class='fu'>simul_process</span>(<span class='no'>x</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>simul_process</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for params_process</span>
 <span class='fu'>simul_process</span>(<span class='no'>x</span>, <span class='no'>phylo</span>, <span class='kw'>simulate_random</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
diff --git a/docs/reference/simulate_internal.html b/docs/reference/simulate_internal.html
index 93bba1f..30c508f 100644
--- a/docs/reference/simulate_internal.html
+++ b/docs/reference/simulate_internal.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Simulate a Stochastic Process on a tree</h1>
     <p><code>simulate_internal</code> simulate a stochastic process on a tree.</p>
     
 
-    <pre><span class='fu'>simulate_internal</span>(<span class='no'>phylo</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>, <span class='st'>"StudentOU"</span>),
+    <pre class="usage"><span class='fu'>simulate_internal</span>(<span class='no'>phylo</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>, <span class='st'>"StudentOU"</span>),
   <span class='kw'>p</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>root.state</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stationary.root</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>value.root</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>exp.root</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>var.root</span> <span class='kw'>=</span> <span class='fl'>NA</span>), <span class='kw'>shifts</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>edges</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>values</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>relativeTimes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>), <span class='kw'>eps</span> <span class='kw'>=</span> <span class='fl'>10</span>^(-<span class='fl'>6</span>),
diff --git a/docs/reference/split_params_independent.html b/docs/reference/split_params_independent.html
index 154fa44..35ff56d 100644
--- a/docs/reference/split_params_independent.html
+++ b/docs/reference/split_params_independent.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Split independent parameters into a list of parameters</h1>
 The reverse operation is done by <code>merge_params_independent</code></p>
     
 
-    <pre><span class='fu'>split_params_independent</span>(<span class='no'>params</span>)</pre>
+    <pre class="usage"><span class='fu'>split_params_independent</span>(<span class='no'>params</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/sum.partitions.cardFixed.html b/docs/reference/sum.partitions.cardFixed.html
index a7c4441..43cacc1 100644
--- a/docs/reference/sum.partitions.cardFixed.html
+++ b/docs/reference/sum.partitions.cardFixed.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Sum on subsets of a given cardinal.</h1>
 fixed, of the sums computed by <code>sum.prod.comb</code>.</p>
     
 
-    <pre><span class='co'># S3 method for partitions.cardFixed</span>
+    <pre class="usage"><span class='co'># S3 method for partitions.cardFixed</span>
 <span class='fu'>sum</span>(<span class='no'>A</span>, <span class='no'>N</span>, <span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>cardI</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/sum.partitions.html b/docs/reference/sum.partitions.html
index 96e72fc..7215bee 100644
--- a/docs/reference/sum.partitions.html
+++ b/docs/reference/sum.partitions.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -83,7 +83,7 @@ <h1>Sum on all subsets.</h1>
     <p><code>sum.partitions</code> returns the sum on all I subset of [1,p], with |I|&gt;m.</p>
     
 
-    <pre><span class='co'># S3 method for partitions</span>
+    <pre class="usage"><span class='co'># S3 method for partitions</span>
 <span class='fu'>sum</span>(<span class='no'>A</span>, <span class='no'>N</span>, <span class='no'>K</span>, <span class='no'>p</span>, <span class='no'>m</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/sum.prod.comb.html b/docs/reference/sum.prod.comb.html
index 2a39384..1f14390 100644
--- a/docs/reference/sum.prod.comb.html
+++ b/docs/reference/sum.prod.comb.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Sum on a simplex</h1>
 products of prod(A[i,k_i], i in I)*prod(N[i,k_i], i not in I).</p>
     
 
-    <pre><span class='co'># S3 method for prod.comb</span>
+    <pre class="usage"><span class='co'># S3 method for prod.comb</span>
 <span class='fu'>sum</span>(<span class='no'>I</span>, <span class='no'>A</span>, <span class='no'>N</span>, <span class='no'>K</span>, <span class='no'>p</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/sum.simplex.html b/docs/reference/sum.simplex.html
index a248bc9..8f9b16f 100644
--- a/docs/reference/sum.simplex.html
+++ b/docs/reference/sum.simplex.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Sum on a simplex</h1>
 of NN[i,k_i].</p>
     
 
-    <pre><span class='co'># S3 method for simplex</span>
+    <pre class="usage"><span class='co'># S3 method for simplex</span>
 <span class='fu'>sum</span>(<span class='no'>NN</span>, <span class='no'>K</span>, <span class='no'>p</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/test.root.state.html b/docs/reference/test.root.state.html
index cb4e4c9..48fc113 100644
--- a/docs/reference/test.root.state.html
+++ b/docs/reference/test.root.state.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Test state of root.</h1>
 define root.state.</p>
     
 
-    <pre><span class='fu'>test.root.state</span>(<span class='no'>root.state</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>), <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>test.root.state</span>(<span class='no'>root.state</span>, <span class='kw'>process</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"BM"</span>, <span class='st'>"OU"</span>, <span class='st'>"scOU"</span>), <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/transform_branch_length.html b/docs/reference/transform_branch_length.html
index 233f526..b5c21d6 100644
--- a/docs/reference/transform_branch_length.html
+++ b/docs/reference/transform_branch_length.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Transform branch length for a re-scaled BM</h1>
 parameter alpha.</p>
     
 
-    <pre><span class='fu'>transform_branch_length</span>(<span class='no'>phylo</span>, <span class='no'>alp</span>)</pre>
+    <pre class="usage"><span class='fu'>transform_branch_length</span>(<span class='no'>phylo</span>, <span class='no'>alp</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/transform_shifts_values.html b/docs/reference/transform_shifts_values.html
index 3ede57d..9fe05e0 100644
--- a/docs/reference/transform_shifts_values.html
+++ b/docs/reference/transform_shifts_values.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -86,7 +86,7 @@ <h1>Transform the shift values</h1>
 to be a BM.</p>
     
 
-    <pre><span class='fu'>transform_shifts_values</span>(<span class='no'>shifts</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>to</span>, <span class='no'>phylo</span>)</pre>
+    <pre class="usage"><span class='fu'>transform_shifts_values</span>(<span class='no'>shifts</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>to</span>, <span class='no'>phylo</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.allocate_regimes_from_shifts.html b/docs/reference/update.allocate_regimes_from_shifts.html
index ec51b18..0327ec5 100644
--- a/docs/reference/update.allocate_regimes_from_shifts.html
+++ b/docs/reference/update.allocate_regimes_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Update function for regime allocation.</h1>
 node, knowing the regime at the parent node and the vector of shifts positions</p>
     
 
-    <pre><span class='fu'>update.allocate_regimes_from_shifts</span>(<span class='no'>edgeNbr</span>, <span class='no'>ancestral</span>, <span class='no'>shifts_edges</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.allocate_regimes_from_shifts</span>(<span class='no'>edgeNbr</span>, <span class='no'>ancestral</span>, <span class='no'>shifts_edges</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.compute_betas_from_shifts.html b/docs/reference/update.compute_betas_from_shifts.html
index 029146a..4d42485 100644
--- a/docs/reference/update.compute_betas_from_shifts.html
+++ b/docs/reference/update.compute_betas_from_shifts.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Update function ofr optimal value computation</h1>
 knowing the optimal value at the parent node and the vector of shifts.</p>
     
 
-    <pre><span class='fu'>update.compute_betas_from_shifts</span>(<span class='no'>edgeNbr</span>, <span class='no'>ancestral</span>, <span class='no'>shifts</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.compute_betas_from_shifts</span>(<span class='no'>edgeNbr</span>, <span class='no'>ancestral</span>, <span class='no'>shifts</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.enumerate_parsimony.html b/docs/reference/update.enumerate_parsimony.html
index 5a64349..0ecff43 100644
--- a/docs/reference/update.enumerate_parsimony.html
+++ b/docs/reference/update.enumerate_parsimony.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Actualization of the enumeration.</h1>
 and compute the solution for the parent node, given its children.</p>
     
 
-    <pre><span class='fu'>update.enumerate_parsimony</span>(<span class='no'>daughters</span>, <span class='no'>daughtersParams</span>, <span class='no'>parent</span>, <span class='no'>cost</span>, <span class='no'>clus</span>, <span class='no'>pos</span>,
+    <pre class="usage"><span class='fu'>update.enumerate_parsimony</span>(<span class='no'>daughters</span>, <span class='no'>daughtersParams</span>, <span class='no'>parent</span>, <span class='no'>cost</span>, <span class='no'>clus</span>, <span class='no'>pos</span>,
   <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
diff --git a/docs/reference/update.incidence.matrix.full.html b/docs/reference/update.incidence.matrix.full.html
index ff98af0..d1592aa 100644
--- a/docs/reference/update.incidence.matrix.full.html
+++ b/docs/reference/update.incidence.matrix.full.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Update function for incidence matrix</h1>
 in <code>incidence.matrix.full</code>.</p>
     
 
-    <pre><span class='fu'>update.incidence.matrix.full</span>(<span class='no'>daughtersParams</span>, <span class='no'>parent</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.incidence.matrix.full</span>(<span class='no'>daughtersParams</span>, <span class='no'>parent</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.incidence.matrix.html b/docs/reference/update.incidence.matrix.html
index fbcb019..69d0599 100644
--- a/docs/reference/update.incidence.matrix.html
+++ b/docs/reference/update.incidence.matrix.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -85,7 +85,7 @@ <h1>Update function for incidence matrix</h1>
 in <code>incidence.matrix</code>.</p>
     
 
-    <pre><span class='fu'>update.incidence.matrix</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.incidence.matrix</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.parsimonyCost.html b/docs/reference/update.parsimonyCost.html
index 9ae5328..fd0fd2d 100644
--- a/docs/reference/update.parsimonyCost.html
+++ b/docs/reference/update.parsimonyCost.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Actualization for parsimonyCost.</h1>
 the vectors of its daughters.</p>
     
 
-    <pre><span class='fu'>update.parsimonyCost</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.parsimonyCost</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.parsimonyNumber.html b/docs/reference/update.parsimonyNumber.html
index d7ad0ae..2a8d1dd 100644
--- a/docs/reference/update.parsimonyNumber.html
+++ b/docs/reference/update.parsimonyNumber.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Actualization for parsimonyNumber.</h1>
 the vectors of its daughters.</p>
     
 
-    <pre><span class='fu'>update.parsimonyNumber</span>(<span class='no'>daughters</span>, <span class='no'>daughtersParams</span>, <span class='no'>cost</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.parsimonyNumber</span>(<span class='no'>daughters</span>, <span class='no'>daughtersParams</span>, <span class='no'>cost</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/update.partitionsNumber.gen.html b/docs/reference/update.partitionsNumber.gen.html
index 1b0ca7a..8558d1a 100644
--- a/docs/reference/update.partitionsNumber.gen.html
+++ b/docs/reference/update.partitionsNumber.gen.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Update formula in the general case</h1>
 Nk and Ak of a node given its daughters.</p>
     
 
-    <pre><span class='fu'>update.partitionsNumber.gen</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>update.partitionsNumber.gen</span>(<span class='no'>daughtersParams</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/wrapper_E_step.html b/docs/reference/wrapper_E_step.html
index d24a27a..de29066 100644
--- a/docs/reference/wrapper_E_step.html
+++ b/docs/reference/wrapper_E_step.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@ <h1>Wrapper for E step in EM</h1>
 recursivelly in case of independent parameters.</p>
     
 
-    <pre><span class='fu'>wrapper_E_step</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>process</span>, <span class='no'>params_old</span>,
+    <pre class="usage"><span class='fu'>wrapper_E_step</span>(<span class='no'>phylo</span>, <span class='no'>times_shared</span>, <span class='no'>distances_phylo</span>, <span class='no'>process</span>, <span class='no'>params_old</span>,
   <span class='no'>masque_data</span>, <span class='no'>F_moments</span>, <span class='no'>independent</span>, <span class='no'>Y_data_vec_known</span>, <span class='no'>miss</span>, <span class='no'>Y_data</span>, <span class='no'>U_tree</span>,
   <span class='no'>compute_E</span>)</pre>