From 387b475aafa1178c2979c717ae65400b2e07be8d Mon Sep 17 00:00:00 2001
From: Paul Bastide <paul.bastide@gmail.com>
Date: Mon, 1 May 2017 15:14:35 +0200
Subject: [PATCH] Rebuild doc.

---
 README.md                                     |   2 +-
 docs/articles/index.html                      |   4 +-
 docs/articles/tutorial.html                   |   4 +-
 .../figure-html/unnamed-chunk-2-1.png         | Bin 31337 -> 31337 bytes
 .../figure-html/unnamed-chunk-4-1.png         | Bin 31401 -> 31401 bytes
 .../figure-html/unnamed-chunk-6-1.png         | Bin 31401 -> 31401 bytes
 docs/authors.html                             |   2 +-
 docs/index.html                               |   4 +-
 docs/news/index.html                          |  13 ++--
 docs/pkgdown.css                              |  67 +++++++++++-------
 docs/reference/PhyloEM.html                   |  54 +++++++-------
 docs/reference/add_complementary.html         |   4 +-
 .../allocate_regimes_from_shifts.html         |   4 +-
 .../allocate_shifts_from_regimes.html         |   4 +-
 .../allocate_subset_node.simulate.html        |   4 +-
 docs/reference/check.selection.strength.html  |   4 +-
 docs/reference/check_data.html                |   4 +-
 docs/reference/check_dimensions.html          |   4 +-
 docs/reference/check_parsimony.html           |   4 +-
 docs/reference/check_parsimony_clusters.html  |   4 +-
 docs/reference/clusters_from_shifts.html      |   4 +-
 docs/reference/compute_E.simple.html          |   4 +-
 ...pute_actualization_matrix_ultrametric.html |   4 +-
 docs/reference/compute_betas_from_shifts.html |   4 +-
 docs/reference/compute_diff_exp.BM.html       |   4 +-
 docs/reference/compute_dist_phy.html          |   4 +-
 docs/reference/compute_expectations.BM.html   |   4 +-
 docs/reference/compute_expectations.scOU.html |   4 +-
 docs/reference/compute_fixed_moments.html     |   4 +-
 docs/reference/compute_gauss_lasso.html       |   4 +-
 .../compute_log_likelihood.simple.html        |   4 +-
 .../compute_mahalanobis_distance.simple.html  |   4 +-
 .../compute_mean_variance.simple.html         |   4 +-
 docs/reference/compute_residuals.simple.html  |   4 +-
 docs/reference/compute_shifts_from_betas.html |   4 +-
 docs/reference/compute_state_filter.html      |   4 +-
 .../compute_stationary_variance.html          |   4 +-
 docs/reference/compute_sum_var_diff.html      |   4 +-
 docs/reference/compute_times_ca.html          |   4 +-
 .../compute_tree_correlations_matrix.BM.html  |   4 +-
 ...compute_tree_correlations_matrix.scOU.html |   4 +-
 docs/reference/compute_var_M.BM.html          |   4 +-
 docs/reference/compute_var_diff.BM.html       |   4 +-
 .../compute_variance_covariance.BM.html       |   4 +-
 .../compute_variance_covariance.OU.html       |   4 +-
 .../compute_variance_covariance.scOU.html     |   4 +-
 docs/reference/correspondenceEdges.html       |   4 +-
 docs/reference/enlight.html                   |   4 +-
 docs/reference/enumerate_parsimony-2.png      | Bin 2019 -> 2022 bytes
 docs/reference/enumerate_parsimony-4.png      | Bin 5456 -> 5553 bytes
 docs/reference/enumerate_parsimony.html       |   4 +-
 .../reference/enumerate_tips_under_edges.html |   4 +-
 docs/reference/equivalent_shifts-14.png       | Bin 8951 -> 8931 bytes
 docs/reference/equivalent_shifts-4.png        | Bin 8327 -> 8206 bytes
 docs/reference/equivalent_shifts.html         |   4 +-
 docs/reference/equivalent_shifts_edges.html   |   4 +-
 docs/reference/equivalent_shifts_values.html  |   4 +-
 docs/reference/estimate.alpha.html            |   4 +-
 docs/reference/estimateEM.html                |   4 +-
 .../extract.enumerate_parsimony.html          |   4 +-
 docs/reference/extract.equivalent_shifts.html |   4 +-
 docs/reference/extract.html                   |   4 +-
 docs/reference/extract.parsimonyCost.html     |   4 +-
 docs/reference/extract.parsimonyNumber.html   |   4 +-
 docs/reference/extract.partitionsNumber.html  |   4 +-
 docs/reference/extract.simul_process.html     |   4 +-
 .../extract.variance_covariance.html          |   4 +-
 docs/reference/find_grid_alpha.html           |   4 +-
 ...egression_vectors.glmnet_multivariate.html |   4 +-
 docs/reference/find_shift_values.html         |   4 +-
 docs/reference/format_output.html             |   4 +-
 docs/reference/get_variance_node.html         |   4 +-
 .../go_back_to_original_process.html          |   4 +-
 docs/reference/impute.data.Rphylopars.html    |   4 +-
 docs/reference/imputed_traits.html            |   4 +-
 docs/reference/incidence.matrix.full.html     |   4 +-
 docs/reference/incidence.matrix.html          |   4 +-
 ...ncidence_matrix_actualization_factors.html |   4 +-
 docs/reference/index.html                     |  42 +++++------
 docs/reference/init.EM.lasso.html             |   4 +-
 .../init.allocate_regimes_from_shifts.html    |   4 +-
 .../init.alpha.gamma.estimation.html          |   4 +-
 .../init.compute_betas_from_shifts.html       |   4 +-
 docs/reference/init.enumerate_parsimony.html  |   4 +-
 .../reference/init.incidence.matrix.full.html |   4 +-
 docs/reference/init.incidence.matrix.html     |   4 +-
 docs/reference/init.parsimonyCost.html        |   4 +-
 docs/reference/init.parsimonyNumber.html      |   4 +-
 docs/reference/init.simulate.BM.html          |   4 +-
 docs/reference/init.simulate.OU.html          |   4 +-
 docs/reference/init.simulate.StateAndExp.html |   4 +-
 docs/reference/is.in.ranges.html              |   4 +-
 ...egression_K_fixed.glmnet_multivariate.html |   4 +-
 docs/reference/log_likelihood.html            |   4 +-
 docs/reference/matrix_of_possibles.html       |   4 +-
 .../merge_complementary_vectors.html          |   4 +-
 docs/reference/merge_params_independent.html  |   4 +-
 docs/reference/model_selection.html           |   4 +-
 docs/reference/monkeys.html                   |   4 +-
 ...s_given_shift_position.OU.specialCase.html |   4 +-
 docs/reference/params_BM.html                 |   4 +-
 docs/reference/params_OU.html                 |   4 +-
 docs/reference/params_process.PhyloEM.html    |   4 +-
 docs/reference/params_process.character.html  |   4 +-
 docs/reference/params_process.html            |   4 +-
 docs/reference/parsimonyCost-2.png            | Bin 2542 -> 2607 bytes
 docs/reference/parsimonyCost.html             |   4 +-
 docs/reference/parsimonyNumber-2.png          | Bin 3435 -> 2710 bytes
 docs/reference/parsimonyNumber.html           |   4 +-
 docs/reference/partitionsNumber-2.png         | Bin 1746 -> 1753 bytes
 docs/reference/partitionsNumber.html          |   4 +-
 .../penalty_BaraudGiraudHuet_likelihood.html  |   4 +-
 .../penalty_BirgeMassart_shape1.html          |   4 +-
 .../penalty_BirgeMassart_shape2.html          |   4 +-
 docs/reference/penalty_pBIC.html              |   4 +-
 docs/reference/plot.PhyloEM.html              |  17 +++--
 docs/reference/plot.enumerate_parsimony.html  |   4 +-
 docs/reference/plot.equivalent_shifts.html    |   4 +-
 docs/reference/plot.params_process.html       |   4 +-
 docs/reference/prod.index.html                |   4 +-
 docs/reference/qr.solve_exact.html            |   4 +-
 docs/reference/recursionDown.html             |   4 +-
 docs/reference/residuals.PhyloEM.html         |   4 +-
 docs/reference/sample_edges_intervals.html    |   4 +-
 docs/reference/sample_shifts_edges.html       |   4 +-
 docs/reference/scale_params.html              |   4 +-
 docs/reference/segmentation.BM.html           |   4 +-
 .../segmentation.OU.specialCase.lasso.html    |   4 +-
 ...gmentation.OU.specialCase.same_shifts.html |   4 +-
 docs/reference/shifts.list_to_matrix.html     |   4 +-
 docs/reference/shifts.list_to_vector.html     |   4 +-
 docs/reference/shifts.matrix_to_list.html     |   4 +-
 docs/reference/shifts.vector_to_list.html     |   4 +-
 docs/reference/shifts_to_simmap.html          |   4 +-
 docs/reference/simul_process.html             |   4 +-
 docs/reference/simulate_internal.html         |   4 +-
 docs/reference/split_params_independent.html  |   4 +-
 docs/reference/sum.partitions.cardFixed.html  |   4 +-
 docs/reference/sum.partitions.html            |   4 +-
 docs/reference/sum.prod.comb.html             |   4 +-
 docs/reference/sum.simplex.html               |   4 +-
 docs/reference/test.root.state.html           |   4 +-
 docs/reference/transform_branch_length.html   |   4 +-
 docs/reference/transform_shifts_values.html   |   4 +-
 .../update.allocate_regimes_from_shifts.html  |   4 +-
 .../update.compute_betas_from_shifts.html     |   4 +-
 .../reference/update.enumerate_parsimony.html |   4 +-
 .../update.incidence.matrix.full.html         |   4 +-
 docs/reference/update.incidence.matrix.html   |   4 +-
 docs/reference/update.parsimonyCost.html      |   4 +-
 docs/reference/update.parsimonyNumber.html    |   4 +-
 .../update.partitionsNumber.gen.html          |   4 +-
 docs/reference/wrapper_E_step.html            |   4 +-
 153 files changed, 385 insertions(+), 356 deletions(-)

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 e5b7eabb35b735573923cf68672cd865edeb42e1..e05f4293c5de03b9f37f498fa76587d3405050f7 100644
GIT binary patch
delta 42
xcmaF)h4JMV#tmf|lLazdHkW105EMV~pZ$X0y_KtXFE(cY0#8>zmvv4FO#r(w5{Li*

delta 42
ycmaF)h4JMV#tmf|n|Ec*5S;v>)J6QjfA%W{_g22Tarz+x5O})!xvX<aXaWH8OBD?O

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 1b7ae74b193833a5a8ffb72a4846f9192bc59ac8..6d90060bfb9971b2fa8d8f45f20b5173f4fe2a6a 100644
GIT binary patch
delta 46
zcmZ4am2u@)#tqF`lLNAhfmm>JbJl5o@eltQ8y$aqTpHTDngIwrUHx3vIVCg!0Q~_J
A3IG5A

delta 42
xcmZ4am2u@)#tqF`n~!Im=AUd(<|6*#KjS`*A0JoqIxS%U0#8>zmvv4FO#r%Y5?ufQ

diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-6-1.png
index 1b7ae74b193833a5a8ffb72a4846f9192bc59ac8..6d90060bfb9971b2fa8d8f45f20b5173f4fe2a6a 100644
GIT binary patch
delta 46
zcmZ4am2u@)#tqF`lLNAhfmm>JbJl5o@eltQ8y$aqTpHTDngIwrUHx3vIVCg!0Q~_J
A3IG5A

delta 42
xcmZ4am2u@)#tqF`n~!Im=AUd(<|6*#KjS`*A0JoqIxS%U0#8>zmvv4FO#r%Y5?ufQ

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 9fcb9d5fb60645b93167bdd3d22cfdbd7dbb3634..75bc1e6e86015127307a9a798da699755a73ed41 100644
GIT binary patch
delta 1051
zcmaFN|BQb^hP}MJyn=#)qN1X*va*Vbin_YGhK7cwrlz*GwvLXDzP`SJfq{{ck%@_k
zsi~=jg@vW1rM0!Sjg5`Hy}gr@)5Im}iYX~6nVFe+d3l9}g(W2=m6eq>H8r)hwG9mo
zZEbDs?d=m^YE2enRMFkEY18J-o40P=x^3IG?c2BS+O=!<?%n(L?K^bn(2*lYjvhUF
z>eQ*TXV0EHckaT43zO3sRVMc_dPEDco^xSfVEy9h;uumf=k1-y%`u^jZ4cGDn3U8O
zSUhNv>e+ULQO2T4BdfrLl_fn;WU*5Lk08I6T&M8!KWVe&Kg6vKy}Enb`QnXw`)?hN
z-u-Kpxw?Sa?|lr@yeDsDc9^_?*{6P^-}~D+>nd+=XLmoc(d&QZS^d6$B@eGG-6&eP
z=8}H=_fPL?{<nfT&hj-+ZT>&Faq5i4zK>ViBU<EZKHUqCJ7GOfqI#k6V~hV=k4Lo3
z-~0Oa?(ZLuzy4?R%_;p@;q|GV$viu%Uj3Xr`SET(w)7(#-TdcT{`ws(Uwgj0+4vDp
z#A5wiv)Q-#;-uyZPF7@JUccrFzkSJNX?>o&j^w#^)vq6i&)e}%Jz4ot#M18VHruV=
z|2%V}%OWiE_f$!3?e52ox3}kPXJ22Jc<gdaq)dE$$^GyR9Q*hEt0@2Xd-i{c*@DNV
z{-%Ate)nf<@$qEiM-hwv@B4i2zTNkum#2eV<5j=obDMe1lS?nUEIb}5bT&^eXDOUK
zfr(Sh`0<YqJKyfx`?py5{qz6#&RB>Yn4YXQc_FiM{pymMw9Pm7{B&>D2D(c7x=nq_
zPvLyo7{TLOwcoeh{rK3LE&Pb#?W^teyUNAi|GjbY<ioNri5<z?y3^%v>~`ON{a(f4
zXOE9JZ&&KOsaKl?bn$Q7U%%eR?ECY?x1awUP@(FPkGsSF7MIVfO(}4b*{rMB=YFrY
zq~yob+3_-S>IIMIcy~Nb06L-U_m>wv7HQE=GLt)!%?fp<TBHdb&v_J~Rd`0F@8*$>
zA&+Kw%53gTUU|fDvPGKk@u1FRwZb!MeM^Oo`#hTAE90%&H}i<$Y>R1LGRB?68emS8
z39H!e@4mZzv;2+k&NI?d3w0XwfzcaKALS+U+`L|HuE6me?#{<2qw|0Me9;E<ft!r}
z{eOFl?@P%7eRsO!@x!+t?|$#^1BONX-pu>;lXu^(`xT#G`RvKQ-R}9WGONG*3|{UZ
zUw<4JZ`WSrr_Zyrsd@A4qGaKki?-~$AKyHC^&pUa;eEc%ow@qC^W^RbvU|#?6i%3|
g&c1B&24+^Vf9xJ1e)GQyJz@X>Pgg&ebxsLQ0EEN}>i_@%

delta 1057
zcma))|5K9%9LGlxTt<*&G;0oUTW}i)BH^<(cuqhO#pIHTyBgv>h+@I@=*70i_7EIj
z=5Y`1o)Sp#(Yzd;9;5^#Hnzy&bD<j+0wH6JO^6W;C);ogw&wK@`1$Si%j@p_y3c&L
zCH%r^Zgg~XOiT=oMx)c|v9YmnadAv0lf`1i$HyloCMG2%B_}7Rq@(}<z-F^K91fSu
zO-oBlPfrIyP$rM1LJ(A3TwGpW4#TiOAP@?Lm6erZvAC+Ls;;h1w!#c-Yiq-{2hbC`
zySsaOdU|_%6$(Xvf4@?x92gi-tJNBfMyu5h4Gj?lF+4o1)9LhjJ$5F59ymKYi=hDr
zKU){eTS=ss?KxTd@&#?nhUJNqb0oq(-9XJRd0UqCume7mReNAzup>WXTL$B43M2Oz
zZSOEoxTyA($U&3mu6q1^(X!L6>MQh)tM%T_&8NBbuV3eZq<akPo1jzJl^_OEaP1wr
z^@pa-B3C2u@d6n2%<08PD8f=3>PJOXC0`_&zi-$9-+Tb!;uWq__bZ2HdFE13p#X_<
zPGl7Am;m>z)uN4-hqR-&NvA-!!&Rm_Yn_=_Kajx&_=Jh<Q}9uhL?HN*uuf*03-Gtl
zWuK*X1X<TjW`_DXL|)o&b4;z)W3mts%X_I5x#7S*?OK1*I>|B@ToZK(7k}T=oX+7N
zps*a5EL~+IN=+(1o5K1<D7dfhHw)$-y>=-((fe-;evSvXdH(9ei(ZlNCkI^{YkcGP
z96IV03fDcZO4H*(LkxU#1Oefxs6x-(KbuR!rBJPYy24#wj?dHqr_IsQ8hRLZJt)H;
zCv}^Dso@VD+TJHLeMR0**xYABpO@Q-K(%4$kx_>X*BiGITX=m7&dt^1stVWhXxS5G
zO?Z3D01X|Kc$dy8D{Pk&DO6jT8uaWklb6Q342sV+f2(}w@5z;6B{TaeHPg<;PTcgw
zG#qsq^lf}}R7Z^<ie7E7G_834ajC3Qe>L(K0WcT7<MkRdKhdxe(LqX0LNq!$n!>xy
z<{<ym3GMC{;Nl@lrW8to<G%yy{1$To6AopdgW6m9X7V9QjTHJxyZc)p_zmJiDHI2X
zzKi}CLFAdqxs<~U^y-TWfEP22-H4i5dSq|rZ_*mOJAugGnlV{W9+E&ukBuImZ)$*k
zKB={Dyhk8x#9tv{C&~w%7Hp;+^rws5O01=Z@FikzBM_{dyU6n$vCZ2Nv18~?myzw;
zWiGhtX`-ZkJt=i_{6Dl89q3c6Jsw-F*WOC!<3_3mH@2qH(J}Yvo1&@JW$V%s1HPc$
l7ZH+!b%exWMS<0kRwQ^!Zs8hIjgkD9v;Tvv&Wxh!{{WNt9C!c#

diff --git a/docs/reference/enumerate_parsimony-4.png b/docs/reference/enumerate_parsimony-4.png
index 29da3c2bcb1f5644eb01c0c2e30520e2e06549f7..01b5ccc1f6dfd969fce55f892459edb203e69f02 100644
GIT binary patch
literal 5553
zcmds*d0did*T<=*oT*1`-b^brD`y@{(=ts{6K5uuq|{W@%#_MpND<8y5onom(p+j>
zN<(u&MN@J&HPFnZEG^Jn*vt(#MBESod2X$l_x*gHdH<cy=Xvfwx$f)YoO7S^J-_SR
zJ7;Gtzje=65C|l1bK1fY1lp(y0&Ph8b|di1wJo|kL7<(HHWoj_BA@V>n4sQ80$*T%
zqvV&3w+d_b?b_fv9$Wirh`96*C4pmc=d+Jh-8rwGR+SbEm0NCku=hgEIH>yQwPI`D
zfcbO|F`4f2OeHE<Dd>{Jixly${iK`^<-2yA#&H!3Vbc*M%Z41(!#1x+h~>NYQ3d2T
zzmLeJra+0`fW99X#ezU3F@>P*Rxr@F8d{)VzuyUZ_1jj^WsA)>j^=FqX_v!>efR%s
zmP6acAV=uL8_leX&o4E>qkDB~n8$(!8+|A-L(k>Ql|sNdj^9#6?@_w7gE#5+<_n_S
z#Qfv_ox*#$Iu+~d6sfb4877~Cr5BU)yYLYCJ;|-{XBHPp7$MBr+1bVAQ>jP&hD}@E
zWf&dd>%X~)Od{T3Y){!pDzSyHUQa)+-P4^H(q-%F`PdPv@AIzjMTl=$*rL1<^Jvt<
zc$I(e81|pWYnC7ZOZJ^f&1<?%Z&4}G^`Lc=5Q~!wou(u>73WbO&g&`e{q?&Yoe=S~
zWt{TppSwJr4kbO%pc`{lBQb9t!rUI4grD{H_U21(0d`gUbA=m_4*;9|7=BF-FR)@B
z7Sf~1*S_-XnLFAIN-!<xBsh_hm37Y=v65$~=1A5G1zzplk?Le;{A1P*cO}NYIAk>K
zLJ&-O_44QL;es)&<$aBg1g5Oj9Yquj)BVZB&D&@nvJo@P+f<+VvG?vZfo8+^_2-Ps
zEX(A}`&u<iHd_-hF*B~A^#|7e_r!HeD2W0g;Bj@cuNIbvNm#K^ddrbyfE=itB2!mu
zhZ8!uua#R2+pmDLDwS1JKKVA?>h62gnrPqCBbRA#oM?twYM6bsO~}UZR~DzJ^924#
z)V>$Mp8+xS?AK1(sZHxRQt-Q-$#QO~u1CoG<HN1-Qy+8N$hgJg8CE?Pt0DR`;1MjK
zEQHd7N9^rS3SJLX`TKTddU$$f3U7|I8n!!DBA1t3_b*J)x!UmE%<SfDS%iUs0W$)g
zc+oCrU%>6dElevn6720%mQ*jk@8}i5o49$(tpnxjj=!&={+CzSM3QiWdcQ<84+evs
zpr}s`qUE=3PSCc!nCaQi%^{GujX<FLtSSy^r$Eu1*^f*K53|H$2)XtylIeTIGihUC
ziY=GHSIgpk=yMcDWAbENye)s*=Q=L#L9d=tEHbIZFx@sT+Sa?j!k!iV(bqbQ%}>yC
zCZh(DgvLt0t*={m#J%k_;yjvP%pemCc-dT61=V8#pLC2yu-{w$ad=Mo>gdjtO%SuI
z%V;%i6S$z~yB;t;qP+%+r~p1=^~Zn<Y=5l+0(R!j?U-piM*4QNZE2E~eX2uTGx+<Z
zKTVuC?->jedO?Y_a^I{v-yzpFTagc2#X+h1XJv+;p-y>EeFU!oKlxgXQNs%7Ye?<X
zBtv+}L!qV8ov+r4q28!d%?o9&gb%`z-Sap$zq<*Yb?Ro{7Po-h{>lb2EEO_;)yZiX
z?TSNK^OmIc7nmH5<Y{YbtNE%RQ9ardV9pvis0DY{63watfp+MxT<Iy9`ougj_fD7@
zJ*J=aMv%FkUSN-(doy9J7B)UVIcX3wCKJC>p(M3A=p=rLED$*csyj2}^N;w|Je;+y
zXPX7W&+n1GCL!!ob{DtPc5!hLeX;vM|5wur4=*>#ShBDwVur3qAL=r6!YOM7#<spA
zny{zm*^uf?<iV*k^+$-wsYl?ejhhr37HDTiM@MVeQBwfB<|t*g0UCU8T!&#g?@_Ao
z7i=%UsIaL|CGIr})?s}zD>NF-wr(l>3v?=)EqquO48zf*DRS!3L6hAidvj?h+gCXa
zIfC^G?zgI7(dTk#u{v%Kw<y}Fz@OBG+Bg;D_Y~7j`FRuc0#|2eLeQ)4R6HX;*9H&c
z#0<{=f>(#nfS2^OKbUwDqR{a2s!h?evudXKUJ1ryFX6K+KF%nsqdjAtq1#hJr>1Hs
zvz#NLfgIyDu;C0d@-HcxKJ3u9<#B*UTw&gfS{=TEYh)d^J7rk@_j+49gcWq6q=vRE
zn5gQd-P(*8|6mX?(*$>d!)1M5i9k<rhQUU{{lH#pS$BAi?<*^zt0Kf;V`V5}kIBLZ
zVdrCguAKSu&&BAl2Z^u0a0*KNN%`>U_;`e58Rmf<v~hA8pkOgTt7$;b`@B!DiWCf$
zmzQ5e{h(g`b7~H<*;Q+E`4!73(P${mMh@TIL$vw*pYpqpjoeZ3Jl_y0XuP>;p7J0X
zNXpo1c{oX_C8Ud(eTv?I=3{F899BLn;v+?)Y1~kyJ3w(98Z@*ZZnsL@D;<i{<T26X
z^ZH!@^0GSzAPS6qXY^|JYu!2O_u=W!x3`R9H(Oo>HjEiI<o`!%4U-Y<PYRQhlh>|Y
zV~ZykD2fNY%qOH}ESxv62s9V0c*&S;MOj0N!1Y?3!(%<KR!Ko7kH#ApW*)WyQ?fD(
zvB)V888@M*s7Mv10bc{hvUXKVp~3Ov9*a~Naxm#~%t`!YnanRB;N9pCTVJhpLOjt>
zn*Mf;Iij4d1jtK{npcr0r*c0(<ly$T7A@%-2!w_6BE33$QIv36WlSdAIH>)(TMaYm
z5A;A_jQF=JDcV|c(NXQQ^Cm8#l%e7sMMkTotE{?)#GLKxMrRKU`D=;gO~g#6)yw0n
zHNE7ExBxQSS`~ejqUo@G-P&_HC$y*>vDg7@rPeAJ7=@wN8dQ3rE!*Z|9Z3tc5NdSL
z$_SVe-0NP&Xioe=Wqng#)nMT>(L#E&xRGRS&yuyyc$o6DOoH2%kTopvX{wW)`C=db
zwTE@)x*azD^<>gC((e&usc6Sa=1DJhmzZF3;tzkL3za1)Z`&%TA6wem#&bPHL^b@%
zWEJe%TjAG;sTc9Ayyw$ht4rNOhTHWym}6s{z%Iew*ygo(su#sujS{&yQH`bx&U=N0
zUkzF;SD`04&70i2wbry+;knOXTBF!gA&g1{J$9!y@U?+PCl>PY1Be1*veo@v!SD3i
zMk4kYn_dMYRwdn3e7QVi8ST|8S+!m;FUdu!7U@`xZjWH2xz8^*Tg96^G50>L9l<3a
z`kr3}M>i6xA{3?!0$?hP6EKF94hQ|Z<KLC|S+KMt(Xt|-zq}<*Mb;956~w`(0j}$F
zP6e;k<_md;L%(K8Ml{VZox4uVe&B9X&P(&0<nOR{_gOD93*y05fjZsIS8XMTH*nG}
z`w|e|&CI*Ku&o6!s4pSqQ;F#;9mquh4!}dfidTnJsO^ge*Vp!U0(E^p6Kfa`PD|A_
zTOPS7w-*qw+*BQRz<)s%8LLC3w?78Zcn*-fS43nPlwd-%BPc+OSH^Pz&3eJj&CS`l
zC)YYrVyEE?fae!vv%gk0ZXq``QdUMQaTm(?ukRfqR$gk#=95cG2!OV;HDWF3C1|(;
zZ-1(icla)>O%1`UZ5A~S3_KIw->pAZH&x1bi4i{1^D3>IENZ64M+5!oLa(94k1(<)
zf|duo>QV2w(gTm~diPlWNZojjj(hb*oM?2deHIrLK|0sP9j&f<zm{bLGq?>9@xY_7
z>*&+$?5`DdCIN6Lhf(2ck3{l@6U`|=m)fRVyYEZ>eOav^OZPVkn+)wV=AM);&{_2n
zU1HU(0FECHui;QjORKbAHziGdc|y=uP)xQvL{u}S<ygi^{#p6;ZUNjqobt~;KIRQ&
zyPmTE9KI6R499)*_uRke`}vzLR67^D^z`<sOGGm)glI0=u_lnUvc$_^xGCKLK5H22
z6ik7`eu=U63>En5){PA2>UTmp_#cRsyip(}JklB7Bkv8{X_ElsW5_TqDes=9hm`CD
zSuTA6-_4Q;&#3}#xlrZFq}P3wD=GJ6p{tKBZyIBVcd+l?ZRpBA4@fDbOmYXAVKj#Q
zwxxW!zaWq@UXg3hk7#>T)N6!n7eCpR^FL3^f;soWWRWDT7030Z;>7Xk>Ug{zpuF~x
zDa#V9Qy^=0F1A52`~3e0K|PBf8`Hhdn1s#Dz33pDtkmvxHe%07x^QdStbMGCy!T@n
z{d?>1cjE1_-qN@KE*5K097;pt*1_W`psF5sv4qtqMG1}3jbO5?%)>h?+CJxmE*Rql
zMNH`1ueow;d^*Hl6q7CHcv7#6%3elAjDOez*<W)PACpKbEe#x~L_~0~LThPbety0b
zB@wExekf~*mN5ugT6@64<A#P-nWsG`Cux<4iCmP16alVu39}8OU(07n#fhtEFaAwr
z=wb5sc~1we6wj!cG)23t=w_ptD1o{9J&3+s&O^##2}+GEXJ}yX4>418h!~rjPz0p3
zthvq%Gf)M%gB3p)w}1Q`sBzpNuZy4_wY6ogBvXBO-pb^8JgYvOZ5}q1z+(i~3m@PL
z6av*81nJNldo`cb^6c@~y%=NhZHtp0E-tBjo1dC^e}U>(zd>(M&F80C^=!|jX(xF;
zrGEA^UrIi6q)U9@>3FJHMInhKXwars=7x*Gj3Q2-i-%Uq97O9z;WvI9N^>4YUG(uu
zJy{)+=Vi&o*R75<9N8Ef_<x`-{%Eqg;OaKz=cT(e!@>-`DY*Y^WgGsx@aFlh!*1ny
zBK!4QS_uxEGgo#}CYk3`#4{Lk!inG^01aPmDuYcW+>AWcEr3#)V&5&a*rRvl^-#+n
z_qfV(WTfriG#NP?)1bJInC#P)DQ(w~MZNw$2Euu1isfUv;&<sCNX$L>%^zxNb}R!0
zS-xa4_3Ttu7a@a<6Z1~$<{Sjj-om_#!td;u8=bhX4;1snfWH$~dNU^N;&mH<#kRJ#
zr3DZ4fn%}(_-!sn!Rr=i3rA!RUC4HfY9d}HOm@6bb*-n!xj1TZvI;#v)}Z)<5m3Q7
z$WySbBfV5RYqgZt1Y2Mr!a&(4nx#5I6Co?(W<n;NipOW27&rzT{c-(hgwq~_@kT~L
zW_opi4bicvu&{QzykliyV)$!s8Zc})r;cd8E1wJW#`}s)K$d%_5ecSF+)la7(20jj
zJYdR#nC>eBrWu-<kwf{m83#~A^cw5?0oK!iVF4~u{RDb$B-tl)Dm9!BnY}8U>84;!
zhJFKv2}Tqt55@1V@SPoOx*S8B24YhZ00yQx`>^8tDu2a>mw_ID(D(L6jJ<oT?OGbW
z{5b|2_hss{K8tCNDX3vX&83K<;xiRK#C3oJ*Ok3^iQx7Y`63bt%_T(4{i%^14kan5
z0djsK!PJq@CY?z$K+iQr0GiO0SP9Him|r>?AiVvxEXx8tRx+qIya8g2I$(8A5zK=S
zwRH9nac*wTk(4})9%%<eeIxQW=>CgAO`GGC*Shoqx<34k|8wLMfXj~<2j?-Wpq#%g
hHUG0Gf@88xeT~Kk@`ua=fl(~T#?sEB^p{Jw{sn|)ci8{{

literal 5456
zcmds5SzJ@+wnzO{TP&bgtqMrA)*@I$EruZyw17-P1X8FVq=<+N0htL9Vx@|OGATou
z3kV?~ATmP+6(tHXCCo!2gb+d?fdB~^AZG__&$&<c<(`LgUh<G+e|xR<t^csrZ&&Rs
zloVAJ6%-VdtSrqO6co0rD=2JB{d_y{jqlFW2NV<z9JDgK1dq&HoW!ILh7owny<gsZ
z_5SF|;x{VGnjZ!ef3rv_)nI*o3+p62ZNBe7%0b8KsGo4VtYIH&hS)Rwi)NMhTUHw(
z20paJrwkbUT=$F2C-*KM-C;9h@p;ih#kh7N=A!fusnHJnD4kcZ5&4~LL;|7n9SK7h
z@(IGLwm7)8!k!{9Z-+u(&_hK953|qio+;jb@sRztqraCc?70kA`24uG!moP|D7^a5
z{@I9yzFScj#u>8B1vj9^vCuV~SS&u57eD<>={dX)Y*sqKZDAE)3&i0y?#Ky2yvdUj
zHr8H-d(A!6ZsPt#KD2H@PPVQI#vMI9)tVYmJC39vQ%mnPP8okH%?V7(g-1J;uY`r+
zYR~FiZ{|cHk&7>W*#U}KdMQo5+~Xhj-Tlc2<um@>IeNi2a}3T_x##y7opK9)SFKz1
zQ|*n_x&AD-@X=S3nx=z5O#4x4#gFPn>!=@Ivbzv=ldYv+?4xjMuu5v-F}MgGO@A_!
zn(bX6dc6-e6LpynM5)CG$B0jPv+}c`GSQI~?_RqN36?u4Y%YoxavK`P5J^A?=CsS7
zS$Ih+mN%5=vxHiLu`UokrY8WVrs`m7s+~dk{V@B18igP%%gHh3A{zZi?{3@C8QqcK
zt#-3EX-Cz)l5>p7!~2r+QsvLSJin`{^?5A1bv9>pHrGeI8an0^9fQN+d_;UEwjjz^
z)H8f+Wal-1#>L7H<?2JCXNl3*^W;z7JH6W>>Nbn2<4O^+u)9xNsu-smg^e+K9B`qM
z#U@1bVgq4JYV0Do`RTosvsVfWTwEyUho2lc6@HyP9znLQZk|qflXwtTaKVtwNIO1$
z)F!Rzn6_aqM4uq`H4@LcIn!bxYYW*9))wkPuVJzL$E~fc_@2wetwKCVNuF8YwmIVJ
z$%yf+G>05LpGQ2^!S~>|4l~G4-A;4VYKl`fx;@c6P-3Chv=}2xn*Z1l1L@WoVwr&2
z{3K{-xsDHg<L>9<Guj;FncEb`rZ7Lmxnj=chd)<(KGN~atY$_qX8`Az0+ylTDuA4T
zj*5i+H(|}uQ9FYVZKoM>p4Nc_X?YGVc(3Iz3ZWj7H<_84X~!*SF)Q6I8cBJhKs%K9
z%i%}>2h7*FG&U$t<=T9ugXYU-gEbP`!EbM<c`=x}|0J9PhcmJYP{HrBdWZ|@o`G$_
z>#jCgGiY_i*Yf`|?NRolOM)>ix_Zc9Q-ExAcg>fo!Q$6y7A*AF39q(}b41x+lg>|U
z?trNWbNf!ODIG*$s0sR;%|47a6e!^b0B$3fN8vP!1eqk;`-n;8TLC!{ff6mz&>Yp)
z4H2wz#rS~v&+=A$j>DIS;wnwbZQO8h@kSkN5;I&?!fS3TEBlsbYX5oTrLV?M=5{7p
zTeArf;0cJwLhFyG0!94;o-oxsVUVCFQI}}o+3`C#kTY1Bg;<^3we>_wXJY5j>}=a*
zH*rgy8rg2s3W>EtfxK(F^9)z!N_f!4dT>D7rZ`<<pq-3NeFN?+;}@S}vB^zHzr#`Q
zn4F=fW3i>Iw8CzoWi;p4eU#K=$O&qL-?d~)tsH<Q{@S|QHi*KenErd59*8F^14qg&
zWS~wej~`7$rrR>jnILi!X}XX!IX?~I49x}~Qhf7Q?MPV4@&&%7s==AT!P1V7`a4tA
zoOq3>+jJtDB-`MzBJ_f90qnB?*5+wuSd`HKcJ!-E<W*xN<>I(t!`@hzx^I)zv&(F4
zybJTWEt+n@Ryq2C<Scgp<f0Xp3J5BF^4Lxl?Eh0W`RSLR3fTG9gH>N&|0KPmT3x~;
z$k41cMl$3y$#k*pZ&K8fb0TTeZ|vEzwYfA0YqWTkO~v*OIwLluE4`AAevMD3S$ldi
z1iOqgR}V!=`(jk;WIYgF^yUggqqiVmEQC$A@q*e_Vwd9hg%v-1>`<UywRYDcJE!th
zbXoLTA2ijl%@}#xQb`HW%<peKQ46pX(sHE*ftR)jZXY}v9u>+xyRx3mltO5zk$kPm
zT1mzlhYApuKK%+6i*+JR)O&Sh`cTW1Ku|o9NX(1>W_0JMKV#qes&h}HzZI*naHo=W
z$ZWm)Wow_#bS)E^sFyQ8&o@vttlJWV!Oh3k+%gzUM~9u`M@cvUsa{>oZIo&K&pu7N
zJcFR=r`PJF?;-}@ePl4}p4lGT8e&c|G-^1biEd{cU6xLfx1Zn8(@SwXnPFhQ*OqGF
zr5SZ?JiAhg1_p_^Y|WmE2MOFta)3G{;FaV~Ad3|IEGo>`*OyVC<JuX#U$FytgVy+-
zj9|&DgT$pi(_yIax?0o5B>jj>CgbYS#!H!sV-L#H$NP#*<CUw{5p&FoA7vJg{f{sg
zWg)a(Cm&0=ZGqg077QA_+?HqoIv2&Fe&1u@IZ$rzb>W~0xRQ|$XnAJ2bl#aHE@W_@
zRv|YYk7}_oi!pdnyGj||WYnM{Ne))Qr3SMTr2~~Px?Mh$ZNiJ^1!|9boZK(R-hvJf
z_t9uM66{gzY)x_ud!ftDP|$cPp41R(MI#qo1mvo*zf3!+6F{b&X!egvVwj}YJ<_W$
zm8wZIXkEl84Zf6vb<w^QAiB=~gXp5+{a8|X1V7tbX??<H9Hbk|WVS~OtNi8~MRCHv
znNCptp<L?2DSV)Fc&I0r75j`FcqR;2$#ZZ<XlKOA79552FwPu=TaCjRDtLbbl0(g)
zPuoCyx83!=&D{7fq;ZLmHhPEmYc0pA3eU7~OfmMkGuQt%TV4|7dTlh!%P(Zbt>pA#
z$opk_^pbto&k^!NZl@@2T6tmctE>CQ8ymhP%<#kfoRB2S%G=)A=x-FaC|#bZkIT{+
z-+Xs9g!g;CbJ=FVCRW+#B>A}go{xtB<$7Dout+{apD#9Pj|W7zE=f>M5yBM=_EgMi
zW|R%H2E*r9ztGpitb2?qn-<A&>>2o@4ZON_z5=Byo2{vV<${r~AMS+|y2px`UKjS?
zPi;ujL%KXqn$HxWJ=^Q|8v8RCgXz|#_})}(M@PrCx?4=Nq9R}bM|Xm-K~{{X3?zer
z`b+8m@I}E&4a%-$^FgxZqz4bc0j?xycfRXj%@wC(fO+{0X$tQ|wm(pk2?BAowMpY+
z_+OIA0MssxFYyoli#gZ&)j?}xkzQt=C}{r4(J|!xS@H$Jh^OI^Eh*a{0ysyKcY&2N
zB7gS14;nrC+$$+5iN4;U&o|hAACNJCtIbYeFzcrCW9P#b$HY;x&5d{!Q0(iy7BfL7
z6@gxI7(uRE2K`FbuvwJJ;J1CPSqniP3nS?cIZ(n{5<no?dOj2-{fTFE)^QU6?#iu7
z_P;IZ${rB~4e)UyNa9rG%OY{Sp)1*^YVdrDjqao{E)4=CxeM^XW(LwFy@2cU6GYiL
z{Xjc5TQIS{P}l1o+HbC6B3)XVY8P@MXWoL}QZ6-38D~uU`unRJ-1#{q1b}7H9RLk2
zfu`^TPP~b9iqGsKt-sNoMek7rD)mSL82RQ~@BcU(GW)(=8S))3?y3P0-h}*^;z&-_
zkn^pcylnENlj=Yy+nS~{0r$RcRXXA8=cj3FEfW<YCmMsjuGyKU0o|Z|Tdmk301)eI
zt*f9hJaVGhwDZoEE&?|KkROLekfa_n<wHL+|94tCcAjvX_B-9!Wq^awtDeL&f$pkj
zzaAX$$AEu+ahDgvf_NDpMgepL9|xOx>0XdYSFkDTQ8myF7mUY*Mz6*pA*m~T3pfr)
zAZ`M+fmlQwKUNq6>qcz$$5q?_{Ak6$_|Z{a8w3WqaG!-hiC=(d!3@Be;8RR%fj)O7
z3NkWm182~C5}2jl1?nrMb-EDd$auB-<`Crs3Z(f*`9fP}W(qN4(qyxpS@NxHI0WO~
zCZ3X%&7i+lyh-D^uP-+Ry7T8J@G3vl;_Cty(*u)R=3Sd)3-_IODjA}ulS)>g_Gj!z
zBX+yzOg0pa(-EQUB0}<^*vTYa>9DLzVz%Fs`U+LZrL0kRMZA+7-QP9sJSzZ2PN#;%
zhvNd9*TuO`_+_%K8ogU`H7!Q$N3Xh8i>H4P*J#3xkiKXLtU8GtcXF(xK1rv@4u!c{
z`}9y#Sn`Z!zVB6CYN0loxJx^`;)Pt-;XWPu@i!HMay@;06*chFe0|-Yo_!doaU-m-
z%OdED4$e&*LBnD(kTDpu6q_Y}u<rOMadviqi+u9gZc4!TpPqiF&#SmnxI8trgLygO
z$PybjbXKd_0k<mgE^L)myIRnLBH~47mcs`%GU%IvrbUv7gOG{2Fpi4hOuLXy-&_Yi
zYZeFCAF9LB;*TSu>yqkO;JK05=vTBD`rJ^I8jnynMf<{YxXK09l~Se=P5IDQ!tC`s
zFX29fT2x89H1(apg#OA1L=Addq5uEl-2P<e^l!8!3{rm3Y&1_Q0`AnGhDUYmkg@V=
z+|z}>-7Su0vo#z4c9|}1!EeSgPBk{v&!EdK2RHe{n{xxWm8Mv|H8MjcBGZYY`i>P{
zeE1cb=JteYpO=1J2X&gc`0vBrv&C(q$td+4M%s<vI%5sFGmhUH^RLjbe>QV5Jv`jA
z_%u&)iaG?!b5y_RzPbJA?}czdPjL$gAsI@55xqG>RZPP#?|*DoVE6(!_v+c$4Gy9=
z`+HVRjcgTba^$=(d=UW^57r<^dyijE7v7$cPjm97R{&@=TDnYzL<l@VRe-fIng{=T
z%t&aDMBzv8{$g{Is5@{BU*+9faL_%{<8Y5@(BGUwk}`Gm1Mr?N?gFl!ksLa8zw~+D
z!{WbI5hr#bMAiW3F$#RB|8!eR1)ugak4RYvJ8VHt)T*VkTLv(rhY`xkZmrD^it-bs
zKx&F@O7`zYEkLC;vFA6aCZ)p&*eT~SUTnm0R+NxCIWUk;-%{byw?JX?jD^>YW>WQh
z;o=2v>iTjtzBha#h%D-`@BTO?0~-rAC6xaTqEQ&?;L`XVa=ek@LyFyqVU*tjsP*f>
zc8i1^Pu&UPd%I7U1EYU$x2>%$E3b~jexQUa@*pz;CMiHHwz&>X0a~S@1NIg=ZmoLK
z`t--Z0;MFt6u$j^p$Tb2pN?Y5J@blBiUyk?48IV|BLEX~MGbv9lt1$>ZkI~3(KjtX
zg+d3Ak)l)HWc9~iot{{Z>@OZ5VJbGdWZ$Y>Sh|~KPyyJBkBQ|+2e^=+#(YchQoCNz
zjn?S|H-wRB=CN~)`^L*%pqU6GK0w>R*2L_DcRmEmrc#kjr9`x2QviF&H3E$bq!YDD
z0mIG=HwgaAC}SUyNTS@;`ASd-p}M*n&S&j(Iu9s`$44cRFAeb09|JTCBBvurkWitC
z)0F2C)Xm=K>haraxAsiF_;b52?$^a^`!Cw9{l6~_S7h5fj&|KBvAk~sY)TcZ%<aso
JfB5;{KLDX1Vod-5

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 6257c32e3f4c7fc5db55da577826510b00c2b404..871aff898d545f6f3c749479faf6bb341627d71d 100644
GIT binary patch
literal 8931
zcmbVyXH=70({^kWF@Pwdh9XBrL;(?`hu(WfKtPdB=txhZg7hL?KsuoW5FtP)0i-BR
zIsrlzBvk2LAbdA^*81M}S*JYf&5x{=d+*G>XZFlBGuPh18fx<3^ViRVKp?Q9f{Ydj
zbea(aI`x*~H1NchjEf!wx&cy@k<{^gzdY{atFxVQyuLa{Sw(l_){{80)3<2N*okxv
z(Puwu(Z?F2Mv5v5U<H|R$%U7ljA$2>@TA8zwicoH<cvbg(!o&$H*TDYed_{-oMzR3
zc#AdhR!rg~%cYyQh1zcI&%Wp7EuLe6n|E#B#ECdQockKqu<T9+0+~Osg@QnzkQy8y
zkPSOM=p|q5d62|)rE{PgVAN^Q+W@UoAO-1s5GXrC2L$T-i)rBoOQ%k^zCM=*8+H=p
z8_3zdF`a0|#$_rdyL5LATzcv@m6*ZDskHzNqr5@CAS*U8jBopfyFixCz<0Om>yYtC
zXnf)J4YT%GR>R1bND2P*<^>o2Y6y!mLS;#^IhNJr$j(noQ$0-#3MOj`<<7BzQn&@e
zBoxz9;TM1hHr%$*AZ%sMKdp64YmDb$m*H^{TUKvRFueFle!LjXmLE)_jr96RF9vTt
z|5bdtSjRL<OdXr4Bb=T+<E_-bTAq5^TZaGShhqDxc3G+vG*&6_Xs<<)*Rt8&tYvpn
ze19qsneeBi$QXp^O?SCF?!Lz}2P~u`>4i-<79~`ZLk*|p%9v)#FwdP_|2x#ja{TEt
z74Jr8Ba%jgnOv1zd<%3cHE909&|_MKsc5t})~L|9#&ncNg{|ppVhJUs=19aVNEDbo
zA6@K1wL5ZTSI*RA{-84~C6P9+XC*#1#9K)TJ?^mEhcYmv`Gd>!gJFFg?`o5j04qd8
zOUroLy(Ynu6YovyT(!9I^V-trc$k)Ex5(;OuYKaRE1`-@k}{r^s!JEwXj;i)alCUW
z30625k3ku;jQ?n3EdiLUtE2OA@TNpAFfMcMppPp0NgnyXxXOR&QNO2gFKmDt8VbN<
zet3>KmQz$$R34X@p<|^bUCqxZz1Am(Tp%mx<se#9vE6^n^Fp>JS(BqKqoU$jU$*4k
zyM8D}`;jsu6eGDe;8EEX8SZ`Qig*3Avw_D&{WxI#>(^{-r1d}Gq?hid%L5Yo0&<FQ
z&rwNMGf96F08=Z)gG?gs#AR%~io(3l_eL~Ym{rE!-cL?ik^!&+V~xv?W$sC}`D7<x
zteOKDlP;2z&JWkJ8Q<()9jQBl6%=%()}p&E#Kmm`{wO26y(J2RxfQsYl!XJ%xLK1r
ziE#G;CYjhndHZw+^;fuuS@68=n;(0}^SZnM4U3eOLMBSS`#P^@LKx!X2b(|F@>{Bi
zzp#7<J*Z6);r2ahO-V5Z=JxUfk*C<JDAKjcZldG+y|FK;uX1Sm%N8W7>jGvnxpuR$
zD~H@6%J^N;FTwT;_=1*j8pw5><-@3(2aKYg3t5rOv{EW*bv8eStsiwqQ~=JlfX^B_
znWPKXbTdzjBIjm0oPQPRPunk`$^wDvbz-QLWV>Pf7y?X18M5eQU7l2yLjF?{h-u4;
z#PHd&44c$Iy_okjqzz^d<f*^M6fpMkLD<m&)!>J5ZlVUS)fYB4^cFuf@8$21wc9O@
zbID6A;k|TlyQ1bAY8nzI_gqiUL{Bd@HjAD?zy5IJ!rj2vv%scY4gXSzD=fs_zbk+5
z0~f;UOUJT<T>f4_Qj*0`afg@bhc<HxDvYAg<t;$AVrOa65_ky3*lzyd4WSW7h}K#M
z>lFlhsAlN`E>g&LZx!(Iy$1;G-cJ!s40<2N;@;BYcPz<iOwh&p2hR&KI037RaQ%2(
zWoIF!BQ=`Lgme2?S7MS9Whk3({d9Bo5;^tdnc4X37wqlzjF#Mljcvi_jBh|RO81**
z&zvK7QFaAq7C8+F+of>j+G>}}0Do!@nve?WNI*_ta#7)(sc`<yPJu}Dqswlu0AmDA
z-1MhSKq9JgQC5&-X!8D#Wcf)QyF5K7)&CyB|067?&fMN!Y7U-8qpMpLgeJM+S$EP7
zyU@BG3gY*5qyhMnSr0~6qg%_P`XUc!JW`*$XhEOg`PNdd_)*1Yv+L06l;Xj8|E;Zz
zzDUYPfZOaZV3D>w26FP@@raqNjD-o9T>kt}?QTTn?!-ky^;6J4AQ~>KK|ZTY&cy*|
z{%Yw{QgHIhCl0L5MvhG5wFk%5F7NwuJ7zAN9S4jz?NZ}U>&OJR+dW=hX?IpjNQvjw
z02U;C<5u%^W`}zm)ehL97eqn#8fo7nzO%;wA^-z)4piLLCg#N$4`3wF*w<LoTQ1*C
zLLmt6U^=q>9k<m-x~*IqCMP{ab1nsV3!NFbgnL;l#S>R{jJj>097a}ais?D<1%X(k
zPV(b=Q$jr>wY<H(eL;cu_9ANIK@WZDDK`P}`*CeCcNiGRu}=_3-s=J2dn~?dlH2mH
z)!u^BYxbYz`@eZJ?mjBQnUE&5i7+-!So!*@_$EZcWAng{W2MNb-VvMD?|orj89|y9
z+k3kBCA_J^KG_bNhWBRtgxqt@zkCHz;j!8n9sS&p<}^INh;zKwr@^1Hey@QhLQX#N
zc&mTkQ2p#44U#KvV}lVR)C!~S^QN6wR#bFfoyZ~sE0sT%iiuABkSF-vtpc&lEFr(&
z_b4tp`g$np=!%<g@`SUn_m(fK41#p0v*3fNV_u$<rz=-r6CwXvMmV)a7V<bYFVER@
z)sv6U?JZ%<54KkjokSPfo7q*xs8;;P%%pFQPCVymm1U>cYDKM})YMXFs;Ak(CH2eR
zUUGgcwfRB<*sV7VJ8ZXQeVEnKNJX=0M-uXwXC?lR@3Tr(Zf^3@Fz)TP#S95D(wjGJ
z_Dq(RxDt}!b_1eWl6&fcK+Kp9A4qArMbAxbIjTC6s=#8}9Pk4&O4h+5Wg03>c`Xr1
znlp{nJL;&vrIy6kk=zg8>dpW9b(1McquT_&tsy6;CMOp$_snMD1=4$ZUWR{hkz;4s
zNXOXtT`K874F2W4(54t+O>_$jJG)IURj6#rU`eGt<;IfolYP@S=lmV5mV!W&&epcp
z*0wd#`?V&E`Y5`~<`<<zw|d^q&%dp}j^TuKZ17ATV;fm4w|!izLm7&fhogovD7Wv6
zi78QN>Qz*FIEv#M2YO+A{Da8Db=<2ns|u<|DGg6I3jctR62Z!EX{R%IXk-KPdSe-i
zjmM&}(r+&1-xT98q0p?TEcDQDT;1JB)H-F})_vSev<(YQ);AvC@=h??O*=flcV6k-
zsocW*bBp+~u(04xWj3`#8t~ky!(f*9kPafcpl0yUsq4M^8`>8yhTeA>vhMljzMO57
zGn?+FyM%QAzOgxnwSGkR&Fb)@&X-7*w6ywC;>M{nGEc@lbXmxSrTAa2%m$)L9ma)=
z<X@^qo%r>p$l@swN7hNvxHr{d`qN`U3q@--SlG!HqvTk}$)0yvijTh<FT^B#lKN2X
z%2GiF$ySMV2v=Q?dwKV1rTD5LB4rGy%vYLOncln9=)yvJTX?3ls;VDt<MM2<^eTYv
zVIkM?B6%Jb_9$DHv)cU{H-%HdO0s7*=k9c;t>Tlh7GBHcP3q9?62jMl6mNO{baTYU
z;eHz$q1t2@XzH{0J@@OE2>e;a)Bjqy(9x=;a9onwTG)(k_}C6ZJlo$e2BNAK00tNI
zk67BwZe{p|f(x?@UpqWFcP+Um4zJQO!}%6|5H>~~Lf1ucn_Z9X=UyS+g4w<J7J4y6
zE632P&ds&1VUb!ws1_wfTN_VeB8?sN+*S~fh+I@$W}6b3#zPb8|GMh_56u3%;`~3R
zO(|Eq*>}Wi8&$k#7AlP#Ysx`^Rn;P*d{pwnfL-`CF!8XoTcIjY6_OOs7&EqF85{E9
zXi@(lg7I!FVpukmZDB3=`OpXBKpK{n=7>OQW4h@9N2J{aaQQ@;ZBM%7=4@vSPs++!
z9e&XX`0n`Y*RQFUUFQ2(os|v;_eM4BtT&~SJ9nBdslV$)9Q@cVfY%FadCL5J#-M5_
zlfQ>+Zbp3mjA!5$%i6wS>-jxg;QW^>!;SV#6RrUYDXi2XP|hKpS}kHRicW*D=1Gjx
zmtq0iBWobCK?D8+e$(H=JJfK_W)nCsO-;>*f&DSfh~Uro&kSi*d2NKd^z*IXwi=*W
z-b$k1s&=~+MX#6PF;?A1R^tHRKN)t<SR#K#r*y7bZ%3C<_xS+Lr3X&rxn*G=(q>!j
zygVszbW{K~#Tyqu`0O>>M=mRWl%-f-$3=!xU-9A(q6qJKYVC&M%4r-d_+AfgvKu=(
zcjO{uoET~T<(QpBGTt4!jAukH?}ghHGgi7B#(l>Y*TB_g8I{#L80_lS?$^7MM!tGj
zc6Ggnin#8qO*NHYWgO32%Ae;o+!zN}UPPTf;t+mp4#rR;pL%v9pe<Zild-o~zm)4!
zn_PS7s&E`jVm%`rjYxGPWo=4PB=qYV8IC&o)&~s-1r1Xqha+QtCV$9nWNg02H?Clc
ztgI((7jv871fPC-8DFqtsUMOZvlw|6tUIeO7ZJ2|$asyxKv#q4UImu(vr^paS;N)O
z0%K&`l){@6iPa&(R^gbOvM&QovD?K4^ttykqcbxX4|mL9pBBA2-c#qge?Jh1$F*}K
z_dD!{K9tvSRi#zt4o_$>a!L&_olnZI(X*l~@kCVk8$MA>*sSiS8!0oNAD1p>#BH?X
zBl!p_&YRQzv}%EvitGw2o$e@_@C!_IKZ%a@qF&L+pglm9%o&AX%YJeY@D@(&*h9DZ
z9vbn(k3{rPB#z`bO5)7a|M*i|QuWTHSmKdZ1+7_Q2xWznk@O2cD=*-y!TbR^GUl;g
z@7oQt_Uz+#GwwA^#E3DhtNq0a#N>*{@yY=dqGAHwN0PS0Q79DrU`O{@{Oox4QvUE&
zYzYoG7U_6*FuqPnR(xZ#SSaPg)|To>L{zeop|Nr9@&%4i<Sj8$lxKH$!me>eTDcFR
zA`KHreZd|PCr#n}Xm@cxvI}`o<w(UELd_r>5yp2Fe7i;II#W2$rRV;%as`?c&q^N8
zs44K5(F+Tfh2}rFdSQI4tL4ycUoC+buI=r?IObD@s=~j(8>XaCZ5KhH!f50%bzSHA
z($6Yk&N_k{$MLIfg6fAWGC$xYsYHef<4O}Zs34o5$Mcmp%M5^XGZ`Ua%`|cptiW4E
z5V)*)Cr!96d`FouH8pkdV)QBp8)O97OK+JS3L2W#2m(;Qt+0&Li$wg8-cv=r2xU+=
z!FiSrY6qnqn%h~<dKKmNg!RHyj^RJ+-W=?3jfvcXD@<PsP9^%J5_s*K${K9^a!Hnp
za~<LgQWua;m2(R>EzMN=`V~dyR$+NI^Ws&<tx?h9B!#!&q8CtlO~vu;#-Zu9llP3N
zlJ8EaSCDQ2=~mAwS10{u6~r~UxPkv*@Q0%pqScGHWm6iEL~q5x(WOJdDhCyA$E<Z6
z|19-N*h}N9eW|yrc%x2YrWlPz*NydTVaMWh-XFW(h%d2ar=S0f)-BlB+>9F(BMr4Y
zmon3vC@CeP>r?la?gg5(Rf^wy$i9)IdlBO$UwiC%v^})!?$bfExA<OcW#UEDko$5J
z6(!k86`n7*GCnUBdw$Do_~Wyt0I;?p#G8u`t*>KfXxO1U_eWQ-77wvTJ5xHd##O=^
zHdg6e#N~JoGWUl+d&)y%O>ZxbUh?)|b<vd?#dfA}T`dg_n+Ju_KErdV$_BN<x+^>x
z4}pHeG|pF7!{F&-3u|P5geMoV3ZGwa($4pm187~lYtr@cnZV@TQF^wR^;DnfTg<dc
zK+-C;?#tYDnSfl$_vE&?^DZpMXL@DbQdvoMXts;#k;e*qQSM7-pma|Zu?5%**K%Qz
zp}*mO{v*Zw_nBw}yE{DrHiapKr~&n;jh3S-(-89gp!VJwKq;SHld+Feq1oBiMdVRz
zkG2P$zyHJntzKW<c3SbIi><PpTEL*60>*rUE>$r5L?Oh{9FW%9TU&bpVe$79Rq|VT
zawgvu<zo3snVL(I=^{W2_a$rr`(kO~%NJ8?Xwb+%vqlI{<@FHyd!&to`m5pg+ZJ&6
z(a!QHIW=S6hz@8gYz}MyR6`pZ8*+!cLEqke<F61}JA4H|-9>5;vzM3GO}Rr4Cnpui
zD5Kz-Xg6f}e0D<pnAy@UcBGq7o_gk`V{7;EC^?JDc%}1jg}v+Y4#qI@JLGUpAWn}S
zq35~MJ*N~AXAPwQO==h!Rr~C|w&^FCx^3+h*LffHtIxGGs|<Lvv(U2F=f}>)Ci{Jz
zO_#W<2{P8viXN}o&6D)g;*9Uf&d$BZ(FIhLcF<TFir71Z-c5Nb)(!EtA#YkxUB<7<
zJ*Ru{{#~K#*M(cnOKnA>)z=cW+AwpJtZX=;26MjhT8p;)=+)3wtk0*!W0C&r%epcg
zjPwrJ(PYjH%2f<26QQRHCt3rbtG|G1j=M?R-Md2DM@Zk1kB_D9$J4To?e8a&Qy(78
zwApbPkMO$A9vc>!z?0yzZ*D%oO!1;z^nVx|%wfKOuUgRt0EIGrwK9eC#&QgS+k%Rf
zt?=E0!&g(B0?C3-X2lJ)IHB#R#+xmSEy7|Cb*AC`**77=9z(_@1_pC2;gF}++}CT|
z-<)SvOZ62IIk?T*>`!?wfCicV;e**^oh%;zW?`XzwcqM1O4)}^jd8eO=&7R`d`4la
z<aq?wF~c5n+TFN(tP1q!o~C1kui*D7x!$YC3ciOo*X>~yW{V+vdlme9mL22wA{dx<
zZI!GW4qyuM{B91514a?d@Udi07KC6{iDq+)I33Gzkd@-|=SM9p-4MaGh=GC0YZp}O
z&lW%C!H>>`)7M0@a4(Jxi*;H7MC(9o+Hr6P{wjk&adq|DlEte%7d?4R4p2`>Y3cg{
zeOKOxbyeYlTq~!*bL;f4bUA34y)>3C^2Kb`WY03##;cfYn2m&vbe%c60V%pJjv(x<
zcQ`z8`Sxkk5S$g4ojv)eJ_u{xHp5`5V&}mCbfc1fWcI$cS-oR}oy-yE<rNfyY;P_|
z20b#Dn16Yvelwf)kL^L7qLx<?Z^2Vu6T^G4y~BgrnN6A(ow^~cgQw0&rTK1%NCgcH
z7}XL!(<obPFX9V6+XCR9VgmKX2Mll};$(h>o3v-Dfai#HhJG<~c{!_cyvhzDLBdNO
z3X(YYcO>(AlTirD&goI*8<Bh5%1e^f*=0Fpsg8bcfhIvw+OK2zih+TbAx+<H6zb9T
zb~w|>8!em3;OR>aSP{5(^`M`d?z=}SOBWBpgqP8m?u3jxczFM0D<WS&fBYB$54`}u
zhbl(EUK|TWTg3vi+cu0l?5^9Er8Z6ig*l<jW@l%4E;G~H7OIeN-?XkECnrO?MuTHH
zbp9d__p{VNZ8tp7=y4Wuz>p$tXMuMF1u<{V-nNFy>ev2U%xG*xQ!h8Z@%{%EeJXxh
z!nu5Bk=Wj$jEPVBg}c|ppW+5DNpb@X&68R~pM4i1K-&IBYoOWcS>cLRO3!;Sc*U68
zum)KKbU*H!&95v0G_$o!k(C`90!T7ZLb^`R{eu$N@BWLutqW0@Rr6O&O0Q=AW#GfW
zFf_1sajeonQnG<~DWQWq-tHH#J|7;jLNcs$dIr?bk<8FC=Cjopr>Vx$6pI#bmP?^!
z%;$uq`M2cc>+^51v7Kk7qw^&}C~g>=nPsvwU|S|WY~Sc%D$NiO=Aid$xZ(dGQ3c>6
z#(Az@Xym+a89L}E;n5l}F`oydlDde0Jz4lOvn;$zPru=}YJ~GF8AQHCoU}(07Si%8
z><jmDR1!C8SK;bQcdKu4asqVq;U!>GKDCjd`gklcUWa?@%JKJsd@xT9Jbu|u#{Dm(
zqkxdl&W{E^^5<q|BNK%sB_$adk||N?mjGM0$|=Vx#R$31&dkhsVu-z2@-;qJ=g$*f
z(v|koq55vIvNkwi9SNnV<xXH#(eK|Eb}95w0-4M_>$Vaq__J9F0k%x~3<;ORB#M`P
zlHyPIhm|$|qpwiL){L3kSX&R*c&zrJl*^g3l~?KxRup5{Y@l!I0UjUdfzow^zrgre
z#C-RFh5-l+FSeLAvy!!D0GEGh3>X5B#~Vh1QUHz(nE&nX*zNz3x8vB-kfeQLN5Y>c
zAizRp^7%?em%(80pKP5JzhS0M(phryWEHkQD+N{vCjeUidWdw`!eHwAY^|&D4OKbw
z6*RD_KcEobl#liMQ#43H+kw0aY@!&vTDVC<ABYEquVkocanaQuwX1;Ubq5YbR<G)S
zP>o6jn~?sgYj?QoFzr(HgiBvfFCGZ=2?ECI4Xp##Xi4$}8-DLuc4=wff?G~*t{qfC
zKSc~~_!~HW51KCy<eMV)iD{&*I{<*-v~$&<TRqaw&d!E3(~iK>-iF7s$FV`Zw<xHo
z)zs7mz2A26UcJzHOcnfl@UKpFter9t#P+!2dQvsPcQfCZE8*vFJ>P;&GbHn4<Kj@+
z*;|YFr5xg;M~?uNKm6R35I>Ozj1xIOTUb~e>?{|c(bpfED<~<21jOtG1_Y3?HnWh{
z0?&|Bm(>yr4KQvbay9;$-<C~^1NfcxuU{Dj9L7GqI<xzO;0i=V)J=KYM`6g11Q=V4
zO-lrmh{p=dLm7HpA9a$^(q+8)`R>JKX8uut7xvwAVr?ESc`knNgSW9)_IXRh3*i()
zb=Fgaw-GRj;4PT7`>sB)E_3tjxw+QXRy3MJY?+$*Bw_+c<A=#g#>U1{Qc^%cw3||z
zlVdqpXz=32iz}g@G0kQrl~1^i_Yz`RZbCGq_<MfLYLyrkZO(Obb8;@%X|D{INK-t+
z5JVY*{AmH#BlF83cD_C#Rd1W0>2x3+04-6s*Z~ZiT3TIQotMYX$2Z`B^@$%|-s$Pl
z5L;H8`(-%3{=yj`o&jnWfgrs+bw=&I;6(^z$p9!}Fc=IzEf-xj@WUw&X;KCp_W8r+
z(=1VDeAoN?`*)W|u^y`vtkMAh)D7bCl&m{H2)qtsg4=Ud`a!{RVr6nC$3AbtNBtYb
z);jn>S0e9R&KqFY9471FcosIR&*!b4W&E6zE%-Gpr9WLK01SywPWD+IDNl|!t#p#4
z;IZmrOzzAf>Ffwhu<!pYH?)2Olb|H5(UTpG5o;|wlPo&og&3(-8`oO^5)*)xv{cc2
zQhqPji4~+BJs;8j+d-}Gr(7B*p_FZ1-O>ol2Z^v}&q^c6?19q0mje<TLh~4M?Jf_a
zR1jsiDDQV-!fj?+LjYMab@|!pS)Nj!U%bR1ut++vV0z#_t6~uNx&lzeIu5M#nf#s4
z*1Uk_*O}YOCrJW07mz7{Ib|^a!*VK7m7_%11dNJCz@R8a>~;T?lQ1LQFCv_MeH^C2
zG2Wr6xt{B_S&eu<ed$g$g7z1_rgf2_G6NL5#gf;)`K3%8jT>OhqN8v9DtI)evj7Mj
zpyjvLP;qg|^#BCR@glWJ!GLQ<TKZ9K{|z7=$l(CCvYNYYFB7jDDNgdVwMDo84z;tE
zfa=At(F%K2H@6OAU`Plxi`dxslyxPdcC9t45T$Iv<g{n(0j@i8H;|`t0zCaRFJMW1
z;57PMPfvUY_mi6V;zmN}Y=Kp`CBx-b;q=?=L3gMP0Lz`oj-z&^a^4**TFO-k4iD0p
z3!@4R8BhQnUj!}(q@LUb5V}}>lH<Oa`)Mt_>po9)?7K2n5=~b`{%Qq4KFU0p)2@EY
zOl$&qVyC3<12RLP`2m2PBIsDbQOCIMiPu6O`SF%|(Fabbmsaza^Q^Ox%$)vvw~mwb
zWz=C4hYcmql>%Sjhp1T5#ZRI{xpaQH{RzTTLiq9y$ErebIK3f$b|k0dGQL2`hmv(H
zJY0&RZoM%VaGGBzuevgds|qhqu0JqF>3&D<U|Ldr)NG2fGR^GG&6|s`?lywfAt!EZ
z9c=f%Q^JRQ&(BXEd<D)VW&^)xW+GBjIQ`j+ifSE4_?Bm1@BC?^U*_-3aJnN06sPUK
z5%Tx8oIQ8)vH6oFeQN3VAM*eIy@i_kfgTO*?|FGW-XV^|jZI)V5;TJf*eqW@NUYMX
zOU)ChAoT>!12@9MBCGu`{<&$XC5YNV?X$u_WQnDKl~6wCwpXCf8crKMes^2&@sdH(
zRh69KL|z~%nx6^r6$YeWlh>0ct)Zvg0A+($E&UkOPyOW;iT_)R+}oSr7MGAf#hQvF
zdBwD4Z{J6(bcw9K7k+^T3Q-V2<0O%BV=}T%P?IfYp$Izx^wGx*jEp~w)EUjC9|6kZ
xz6JpIJPICwK{sgssv7(sS^r<}ejFk{o}0fDlbY)WTwVbw%BsnHkb3(1{{e?tq}Kod

literal 8951
zcmbVSXIN9+vW{3l6af(tkRYNcQF`yvm0m(`3IY<E(g_4qnsgNDy%W0hB1BPo=mZE=
zn)FT}K!Cf^@80K}dpzH{&;7agT6^tTvu56zd1nQxsmPO&(vgBdAhIWqWi&t_qMIPl
znFtah;0^2oJ2eP&3-m-r66%(?I_}~05m&#yImt8RYxtUii0Kv$^Uyhxue?&E(5vj!
z>Q-3U=T)PFGucKh>2vzm)K#@gjQTP>YVx#R#uPznaiGE&7Rs6%nU9Gchp3&Smy#-a
z{#eQ`5}hdVmQp!ci5(@1vSe8wVl;}2n<ON2;1@kxMIC!T8yAB>k1hl+odJQ~_-LE~
zJ(fm-K$&S!5U5WL0s>jxrv|;|{YVOWM5k~bbc-yD2o&M}hiNu>#0%2eh42$UnlOJq
zAuaOTVE96`a)JdinaG5hzNc*INQ>hpf(cEV4X4=bVI#MVuV|a+R%jAbR!;tDv3|67
zFApq(j_1?Bk>D?so)J?{&bF}MJ__8+2VT=*k>0jykmkUUl^m;)Xf|XX@teg6vW37E
z8YJ*Mz?Mh6_^|751?OO0i!Uf33it;5^kTevJxh_VZ~l!tutpoC)j^lxdZEb4I~3IM
z$$@BnkjCQMzP@}`)=@3hGd#EHdo<w{yyhN3OROQ%NGEK!S2U-$myN(0zL`Fy{%Cjp
zuZ8yY8oPhCbgeftOyXBUt0cS)fVBcN7E7)A(_`3^hC@Yu{*2!GLOI-eVMi%AxzcI6
z&u)yXigyU5;75h~8&!W(3<}jW8ehN#6&jQcggvW(UAq3gxk(nuaCQh#t>(DyD)mI6
zo&hH88K&TpDb07;rhUUF$QwE3<;}}DyWt2VoI+h!x8Bykbt1seSc*S2r#yQA7-=0#
zJsmNswms%g>9|ilL)h<DOh&jgjN566y<3=^M8eN`p2faSmf+amF56D2Fj&naraVeI
z5-AJO;DSP-@0KW^YCJy+PnRMrUVNf5aQ6RUIseYUzQs802Sh~V@G3hB&JviPV)AA?
z6D$?6r0ws?7B0F&WcqmnnwZS1wA%9dyC+s0X|tvomzKtOEJ7YXsgZ2AtC|qjZx`o0
z3)qtLS}iTJMdnz<ZSyJv`N@$u^N&H3kChp=hs_+JzmGUlm<9JqD4f<^=HHr;@e!tB
zriEj5_!T$1-3CraTStI|3HW1>|65kTj)c4x@nMl7(-&Hdyv?1ZD=5;tjB;Mw&rpY~
zdd$8jpG550)CnYsd0=B{^YZA*N=ehx4=N08>~`rK4V^-49(6M_if^r9T}SH|SLSwk
zn2of|w6rC)p{U&G;LZsPv#`-14J#9=#-5N6$Gdl}i&3Qo1ukRN^Y>K2rs&JA<G6zc
zgo&4PTSAi2bM&iTE@0mmrKz~P%s&>e)f~5%j+DOY4o?t$UdqKYhC47iY#4K0eXH}F
z#+=@9O#7pP{Dmu*Ymd`MZC}i*#!|S?wl;}*L|<h3**PlYyrjk)9u@|uo%ROr#zF9!
zg>=fbBnqLa)+T0;=v7K7^r(>iQV&uNY@`OU_~|ra!><Tiij5Aw5}>sz%1I7LqLR>W
z@hL0piEYh7N&Ehf;;tEt$=_T2k({>n*TF(PjY|EJTQ2R_d?vDq&;EATk@yO&c5T4W
zm1wz}PBBD6_hB>|y&V@fpS7Z`p|QPEww+~jeh%=n(}C0XJf{PiTPp-h1bYUQAZ@$a
zoUb$YnPUisY5bO?QTdh@SQ<I5>w!T4OKW%1tzBM6D*!7C-qfDp3v~hZ{z{kOa|Rgn
zqXn-l`z9oWgVAH<TXl7ASPX-Z!>3QZ3*m+S`hY8NH=x~CzO_uJPYWBn%uc^={wZfB
z2cyYK|6*O7B<xvzi=$YnUszvTXJ}wxmJ4=2mI&~#A(eWU>K`wS^^#eHN#%_+jUsc}
zN{}Pz&}%m&ydo&lOEz?l4zMD+m2l^S4vzU7eAkrT02YInobjXZLqS$7*N48AVixmF
zy4<n3X(L~S{%@fDC)XqY$Xl$LqmY+RfBW{VCu#==cKaa`E+H;|P|0~25LNSTP9A+8
zbEVwl$^AF$q8s?cmQ$6YmuXPdSi7p`mP0%&)b6n&Ju^b}Mj#+0huyK?I4nFoD5k-2
zB(}Wk;pyZqk(NpKc{hyamk{8T#)OVfUm#zC{^Wd#x$8vXEf0L%=Asgh4o@(Vh^|D|
z7#<2GADc(vEz6WrpFeE3AA7H^w~1S}cem2!#;8M#DCm{|{L(Y@#LU4K+Qiv)>hVj@
zNZtTiQ_W>AN0oVRVoY^>^6wp1FBwhe2XXT#WL=VyW?&!kPhQ_f^XM%PS?WL3@2-0L
z1Tc(?&c3z$JGm<QqLDcC0UCF`b7lS^TAUH|CH&lgJ;d4B*?OqRxo#YO>E@M|epLwu
zIy%@a^b~q-FsCYHm6kemCwFJ7n&ed7x@S3B?4{LwR-RFYA7pk8iX>r5>^k%QeI(9~
zjP%0^ll2D8^Rt|w`P2A&&J*djw^lzscOZqk!5Kp!piuiiS9DD37n5A0YYi>6!q1)y
zd&C}<o*sS$Y^bRZH^klIjH#_HJv!96drt!1EhZ!#z=GKLs(_(7^M*M>F)RJ{kj14+
z>{~5zB1cxXPB8C_>35WltGgw>zQhk6oM3xi%Hq@>z23;7!ewPuxOm93xy`i;OrUQv
zqBKa}r<@#D4MMdC4@I>R2+b-BUpk}q=8|Wu>gxTdS~C^hVUipk!-!Cjmc9Y3YB*F#
z8xgrqI46o?jS8jT6Fb^rGRe=g|J>UW<m)Rz!d1c}KR~pg-0ALat}6P9lj+%ujwbhQ
zJDVdRkP{!hi%0G_7~(4+A#t=Z6=2!rsZXLDLB=HW!`y7LIfq=#c9xQlQgEvEL5Iim
z4=MoY^x3=WUKuZUGi)Si(25G`l5CDnX8Q$*;0CJ=%{l6wie?bWo(^`;XE{>>M$6`%
z;I-j}gjUDyBeS8RF{3&M1NP`BBeG25FuUg&X=z(MX%&2YvQ}231}2tD{J?LS-AX8?
ztE^CDuKx5dtHpBmGE)=<emrV+TVw2AZ6B|A;HuNnRGM#oMho)ws|(ZjAnM3~D;R`_
zzPfs^BFFyl{94_NTsU}j`y~y#VOy)<WD{+tbzkOvCK>nrT1g+Gjmw%kWxZo#_z91W
z0P++b*R|ky3tJ;;erWe?lM*pql24{vL1}4nymNjJXt=v9Z@j!^rW6!^$M?R8j`)2y
zwfXfqfh?ld4=E=NE&ZZ)V_Wg@>Cx6w(uk9{M5#RYsdt3t=4xU%=2u6Y6_@!QXnW?p
z1mB7{=Y<?Y>~Ue3zZib_z|V5m7Akh0B9>?$0i=FD=K<U1Pbkcs)g`u%VCRsqs-oWs
za*id%f<h?OvaV87J8zm6wPYMRCtMHC@;*713p*Eii~cniQ6AKnLX`axITm!8;ziap
z4ZCr{RjG&iJMkD;PlEj=(mY>^&Q4>qD*<*u`r`O$DV@T!*E+ahsJ<pohZ;&v!W3WM
zX;gcPncoA|eJ-5W(ZXEJ5bsT^9Axv|fV=<T6ahjCRR+ryQZQ6Y$9$Oh>p-ow>`<8`
z@_vbf`E+|!pd5H}e?I(pD`p*Q^Le;?1pt`>CBqu--kxGBx8sFvl;?U3zv2+=?VU6K
zF=bh#Qb}Q_k&=-U&#(#~wNbSh*-2Xpe0m)KdzF}!>ryh}R7kNRY;uY1!AnicwWb8d
zL*JBR-l-LA5Rmy9u(KQ9$aew95(D6w!a~@wX~J6d_Up5=hZqgVd8k7WQl_R(@B>tS
zGLeN0f9gFhVXmXe{yI2E@-fl>Hyi&GuyZVOSB%%Gu1_E=8hszvjAmztJy8mYuCv@D
zESsFf$MSOB5zY)alu^09xqXuFbAH0Y-rdffJlqs=CM8sRiuqg8*~IY%kIZ)=-XaaF
zxCx8(MqfV>*R_?eFIXxLch<%&T~yyC-f|rs;6euW28shHoV`0684$+s;6uaeNCl75
z))#dh9Rb)>Zk%f8%IewrvYn&}ao?{*;`D`5W>WSZ+x&~8{MrJ>*q5>gl@=SbY4^gZ
z86tsiX{}kQQ3B@e5g$IpU!nnPh><7-0FmV*lcoYpfnC%|vaMGr=d>`Hgg%AMr9?C8
zyXFFz*}BiHS(&ZNFt}`g<T*c|(y(FmEy|y=D(o>f-jw{)C8i03W8=;D)6wU-%1nRO
z3#)z|TTsqyMBk^5jmc??^s+zLspt>zw#UCACQo!bmYH5EPU)+6!uJK9c$n_4TLy%a
zN^Fh=swN*lZ??A}VJb?jEB(=Z>21baKZ;#17xVrM*9g+cnMICRoz3^A^3`T5rJs)c
zcM@u0OZ(&V#VB0gdqrlNkekum51rgzG!|d&S{1tIyTR+e)V}0@hm4j&<msc8*AdUe
z5Jt3Ue`suCjhE*B__~+tRHI*PY;2_f1G?zy#S~hJtJm_{i-T@3_HH?TuYR}m7FOJn
zuU8&zeGtCreQZCUzm@-%+2>^cK!P4Z9}i1_b-)TG2hk@{dhXfW5GKgt`^;pNF>SUK
zM5)U#Yb#-r@UxvdiDv)q6-w8S)nj+1Wph7COUC&>AlvP+?uHJ3TS;b7?Z>cq3|Ck;
zKLk52wq~8g9Z6{CIFD_;l6seYkX_qX>!p6gQV>hQ&%HA1okVy#M;yHOP<xm75yvfR
z7Rw?HT0Yo7ESK4Y*WqfVz|qt&qt|g)H}U1!Nt!cjWeh3i5|M1ak0%mWR@R+{stt-<
zhpPGVEiUZ~e~On?#D3tOIYDp0>v7aLcag2cvx(An;H_^*5;l6A+sL>Rv18QogCzhr
zXitbGIo?N+2K(GQ@$jorXcFDpF6QNP@9VpU8s+CGF38T7T)liD!D&77$({;qzh*-%
zZMh(S&T@#RsATF{VYdSb6Z^c8c-8z^C#pe@MBTGo&{WFTqE{h2hJQ#ve)1}tZ;9Z;
zc-gYyyAm!DWEG8eBs|X``m-i&_FKGJt4hnEogy5?4~w(Y<S@O9OS?@i@?`Yav*AGv
z><7^c2ki$0)Vu&jAPK$+T_HC$C_33n;wZjuLKb+X&4X{f!xdG~poZ`q-Q3&@p^@Sp
z60jsZ%)q~RW#(+Q%Y&8v;4j$7;E;2h9u~(#%{HAe9pFc{9GY}Qf<l(tkJrX658@6i
z1Mp6h2#@~$Ze+3)ZE)v@O0m_RcxmFHn>XY59okQl`y7tm1Y8+AXe<=SoZvj%E0dVm
z`9xv5GHzx77EiYiRB_{cHrb9?)88wJ`_`~W*vnLv<saa-gy<I})Yy%qo$Jfp=f|t|
z8g?8P^TJe+Uj{Cy(tf^U)>c(S2=_jg?;y{(9!6L3a-hmC6eS^keC#6rh~kV7G?q4t
zs41R4fxc+xpyo_*%jjspBaTge4-aOhHCWY-7}I^~Tt2srAIM}RE*x`c825^u`8y@I
z+4qo2fuwxV7)RFm-A`4-SSOP?T*fRT?uA-zncLEIdkaKFw@017OY7&XVeQfGCrQaw
z(ZS9n5uK5bc+xDQsN2lUuB#)MxG2pNPG|HNE_=d4Xr(~K=P^PShJ%cZ0pjr}cW*kF
z!{u{oh7DnAxZC@<OOc}xEc|h=iq==h`=8>4V2&v)#Y<mbO)bkRykmTK2&Lk_#Hylx
zAOHlYlxQz~HLX;!qJ85LYLv=8PSY`Es|F~XD=MrlKOe)_lm%oTkM+YU#$L4u2GUDi
z1irDhEI^3u;Sz4!eW=dCnAV$(F(m0dLB@{sWl;efLN1&%mJ)~~zaFZgn7?4}4}8p@
zBEWy1X3{q|`t=gA34YekH|=5`@q3H4g_`~VWgRiuTepBvz4613#u$Hx=~?cQWM-U*
z>(0*NH%}n@_Z;2btQ^mAU2h-Hf>T%xb{lq|4Y&pb$V%HoAcgI(bD0C!op{``r3S=7
z3C!)j9#`KP&YurHmo3eoYPmJb<gu4*W#<LO-IAM0{8zGxO6}g#0|;aSzFernKFDjk
zIo%}fe|Zt}9u#{soZjI)6nRtJ)2(BI4FGcCvTFR}SGu~xrRE)Q4+zM@1-~)HX0Y4*
z9leB}o}OkFwR3uysvt{3$;SpGh|P$U^(}Ai?s9?%QqY0&&6)K@v_kPv|L8Zo$ggT-
zQ88<p+QWWw`Jgcieg$;QByqBC-yn2|(XofmCuOk@>0xH@0Sy`uSw?CGL&uUGH{_Be
z2p{n0JbeFjCUp&U<<kT<!JaOrGYfaKvamiEly7pG7L9|WBQ~Cz&q>hJ73G54$#<fN
zvG}M>sdt3EZ6Ia;B5|2M`YN^aY8juRqGMyDoM6%vOn&Q<mnLN1Xx@*ajpLpHn|3{4
zMNI{BK-dZ)Ie)?g_j2)@c#PJd4!r&|6#ZE^G8Eu{l-3CDF%-9j_RaIP_VnULM#kPV
zkM6&Q*NF|-kyAG&q@;M^H@@*$inIB$`07?H9R)D%9?8JX%@LDm|H+T-wx6oZlRFZ@
zJVsRU6Y+#C&zNc#@bN#uwx|ns*k!0izG+hMr(8;axVF=Z+tH?-G8wZI3w^z>P3)L$
zRg;B9a)P*+Tz|Nnmsible$2Y(E;ejs#nP9etu3J?%xJJj&3&O~1ju8{%U6L4$zbq%
zi~P9T%ne{cmx2ZS=0WlaB_RxuXGOit@t7xPhR+*!jB8U(w%K>@tB+(E7eUV8_LS@F
zv9~AfO-DX^ZwF3OB_&cdFDvoGFJd`sux0Xdvjoc)>*E8R^+;8(zOC)kKoIX_-_hOK
z8M<Cy<%!=Aa-46-wK6%m>N$z%k7hHN-R?;cSeJN}UR~#N$c191261Y59Up>Kx2s=u
zSi^$!i!PGkj;OU#p`cWTf6ckQd#e=Y*34Y<!IE*lG*tR2xq1?gM*xKhJEbE-UGCns
zRZ<uM9KGr4Rbv~(Rr{lZID^W}gU^bSkf?@-1C(@B*SEj8f+?iX3}QMsK~72lHqz3<
zVq;5)!T2x=)3veQq#DIXQ9;>OvH`)Ook<7Zt4b5OZOeN(u4}w_+ViEhrxwREbn1Kk
zEoEs|`s%&U!gFePf;-wBcndYd3*S8Z@g=pkwg>Q5mt%IIo^kw%#)8Z1%kok8>>Boe
zPTVAZ%^1sL*|obWnPhw{1{M&$4wM6Qbn)>^hpZBy7fmz%hKRW`6bN(yP{Kd*$Y-3>
z8)B-(?20!mlDnZ|kHbG=qWSm*@{(`&0A=>8Ix*woR<vj_JOa%6Am7$zWgxiFKpoPM
z1QD9U!TVjZk>JdnMg~uM-{+^vcM@b1UT<Y3qD9`PIW-l=UYG*_k^4}WE6PnE&*bBh
zB>Z`QKmu&MA}@!87x=(s?ep@uE9za)QV#G3Z29815q;N~H7O*X|JI8yTh()UISa`7
z<4r?#=l4sjL}UQao;mwAnj>6OOjcEFZ%iU6D6h_m=I?1vfM<TdK4ipR02zy@`3n0q
z!L=5a8G8pq_4Of8gcvp$>geiLJd@7Gz-nf~UOjojCB80&+@W?>c5c!MuClPDmU62%
z1`GBC0ZfIFk>;yS3_$wIDDvN@E^lv;Fu;*;vH}N=#qPP{*b_DXm9JNVLe8H*fA{X)
ziVDwj0u6<!si_;#XH9;j7@sdrt^U~91&oRHU;!&T`xR2s(@fg3GoEkmusxhyn0+u0
ze4a&`AKfg2LMp{^0}x3wzc={^w3w|FcN_BE)eMynr-;3R<)o)NH7_ZWd`uqjA}rgg
z@xcmz-IC-};pg9M00}@KZ~4Dv<Nu+J;H3QWWy#Nz!9s(a0}gHwz_cxDVmW(>6%K;+
z$}A8khm%0`3D3;V&I2=Xo{oxOQ=zrZ7G=O53r$eQ0O!E~XaoVF7d<-v=jOz(VE8!`
zA75tK4Hj~^BP?7yW8T@>X;(EG`~K-wz%*Lr3_iB=DMmkR>+D=bw<jhhPJl0D159~<
zO}Q-6kcx(8-l4{2ePVpG6cFkz3kx03Ri(E!K#BVzSfi%du1X|HCFNv_?Rs!$vx)xX
z?+=>-;eXRRS$t6J5ZScq!YJzY@|!;y(7|}$6im|{%O#Dw_QoGL{gn0#S$%x`39Ade
z8S>#^EwRUYdWG6`<6UP1oB)vzp#1lvijYX8x)_ntskH#}f6+$&p>1Qhz1hM@bNzbW
z?|Sq124@^<#_Xz=Sf9%Mk208;n6&e?aMw7Q0qs7|VEfzl&+l|Y;Rk*;QnkDbP*Ld8
zvuF2#5Bti#4qYUUXFS2TP~B5maqIl-z8ymQOSST*zy`kbZgovC5`GW|({N~uT|)Z-
zoZgPj#tzNjG@Ld*Ok0bB!&_$B&}aZe_5e~{n`8<H*CN0A0`Rej(8~K!)_Hk(@$vC}
zeSJ^>9W1*N)y1Szndp0@`2kk7C{D~{w=MGCBz&0-<Kr~B*q@_Qpvz@9CW!GlNB7ru
z=i&j^iHL~!{#^!`lag&!cycN5_ws`3<bN5O*+RdGo}L~fV(0xtA@P-)oDMete&jW{
zbjsv1Thx$=_t9)yWLjF<>co;uUFglfObSnvp*kQhD@%4$uw*;|W^GOO-^PZg{FQU4
z?|+!y+S-y1xT2+_6Mj>O`|e%YsXK4d=G<RP94)E_kTb5i&85o*D;?9Q@XrDrDrPbI
zc7>*y&CHw})f90AknsS*2)>&B?t766N=9`fQ6&ch>uhZuuCh<*j<PuRX2wQ@{ZjS)
z2T{}0rUBo$Tvl|Mz7HTZB@Pyt8+)ZSb5v|$Fby%kbI+xPe;s7nN}__6mX?f+Oh-2*
zB_#%f@f=~$2XLE-{^#E6B$SSh4oI&c5D0wcX+=dv@O3trSj4!U{XReodx$1~!N)*B
z0N*3c-?KEDHT_ahyU0*aTYHe6xTCf8#SwPVsj}hA*s6<lyhYij<nwH~Q|C*?RGoOd
zh_8g>mW+jmG5I<iMzsT5j=H+B9dodK?3{z2pWmjHD~tTE$x)>rfIdZ0adCHdcX(hR
z(71rw*w}R7*kc}uh>YUh^E%pXaJXhh8e0HI0I72dpbxJr>g$iB0h$Jj3OdZTvTA1Y
z^74`}0ovn495~I)*J!>oc=(xm;M(cYlWlA6JI((1>J#%&Z>#XZ$yN;NGFWsN|I9(a
z-VOrcKCXU2b9(yE9I{1PDxSAp&FQxyyfX48m@VpbV;U2GufbUk<yG$J>?9*4h3#pJ
z+m>_uQVStCEeq%sW~UHl@4>6qhCeZLaCEo2KLww<q`x;;IrIWKc<k$T^5Wv6+?BJM
zzpR;Xsn`JYXPPM6W1D$oi<gg2Tc=}0xlBK4YO2)5=d?!wHTTijJZr#w`;Naf$$LVN
z^mYnDd)i;^)cNvk)F578z&CFS*^PZ?JXRa@|8(hk>j)_fP?>rZnL-o!@Y}ckO39**
zNAO=E<-$&G`-OWz|M=hci({_s)s77rJMOOAI}6s<OKSr3F{1waZ|Efm(0^1|&nqtQ
zwBFxJUe|P3f_4kMK>~KQxeUl67yAkBJT~s?dbsATSAJiZNpkvkOUWx95Qb!mSx)92
zi_77fcEC5&85Hy>;0!Z4*dH=t{{$eGW{5+=cDJ>)HO{U=zi@MNQ#&8i`dfel8z8tc
zel}h&6qpos{Z3MU{$5A>F}@0Q_uf5vA!_t%09#GEE@VxQ#%^pBva-Uf?8IEqGn+Sr
z$k9LxLN%om7$Y9jDZb7i5?%Amr+}<w!ex|f@~Eg_Je2}42Q46A5nfxA8Hs!F*QGuh
z^xysQ6f8&tG**8N)uJDK&-3wZ0xk!Xp56tRuJ@?wjHecP`kG7LP}9%`{ia9y6z^3|
z@qRxyci{xF*|gcG@t5{@kTx6QQAKTqxg-FyzyI`dxg^lwRW;90B`}F()RvSiO*aXg
ztWGvK*Y73J=rp$gyjOQO>bM<|z)yXJZeXo4xmk`$rZY=%i^Z?^fAF(WJ|q`E9o)V>
zk8-ZB8pljRjdXS0=M?G$+!GS~C_HEUPTTsw;dKA2b#aA9{m}A}rjk<2UcK4jE-jBm
zxrZjgd~WdFyE7T`drsoHK&1x+o2LKOo0^B#&ghai%uu}v1$4>S2Iw*&KW$3wS=vP5
zc?{++L+`f)$X$G@)yPq}czp56NW(0)tR<Y$e)civY1xbrqW>6VpRZl0@!zqq^N%K}
zGC=>;$iTov4+#${7CPJ;dPwkSJoRk66`<USIh>m>1*6Rv{%dn+p5?y&mJfN?WTi6h
z8iD~hD->V@eRXe%$rOw$+G)Xd<QLV&I{4x-bahYPEU`Y~PwglMgxsm!N1fFF)fWeB
zThyKOZ<3P#e6ix63;EE%hRpo*bSaX}R_1WsLTyahxoW>lG+oJJ2DocRkN7VGO3sPI
za;hT*Z(hmA9JD_u&IRAu@bmS>51l2({_5bVSV(Wf>n|vs1ua|>{6(AoXJX(V^0j}u
c9daxIEuPSnFfI23F0_E2$g0Q`Nj-i0Ul7{p5C8xG

diff --git a/docs/reference/equivalent_shifts-4.png b/docs/reference/equivalent_shifts-4.png
index 1d4231d41348b45d74935dd9c00075760ab1a2d5..b2dd5e10601304d7b70a327212d1b9f99bb3a529 100644
GIT binary patch
literal 8206
zcmbVxcU+Upwst@e1p!g9(M6;;F`<K?w9qtk>C%)EkPe|(5EP_I6G9OsVCcOUr7BgB
zVhkN2w19x5&~jgNfBW2X&fe#q-^YJUX69Wpv)1!GYpv(E^fVahFVcfRAVw|Cn=lZF
znjHk9iaSOPj5r?^V+Db@Mzn6K82YE<Cjz_;eKLs~)<rz_k4oFa)H<lzP95Vp(Kq_~
zC8)Y~M&j)Y!V6!n`L9KlyeI8nt7O4XE<KVB{9fi%x&2J^jXqXWdNJ(Sv7;=<-qFxd
zKTy@|Rn?3STSW&R9J}P^nLtnW46VtZEKyc499f^-WmO*KM<WWl7q-Y}K%i5r^>iQ*
z4KtJ$#2pT!0zJz%1cB}fu!0_*|L=zK)~HlJ?vc5QtXq_Ygmj49%jmo-BIXb^;u#Vr
z=3zXUtIxV6G}zEIaZP2|;B@94h=W-~j{xh|HE;kD862yW_6Bhh?9k0vukn70n@wWq
zyPGostem#_4w#?FwzqTt2~1KyOKHLlg54U(Tjr!mz5%hx(I+ZFka+Si&WCwcydMn$
zwcio~fg}^@LDx^9s6i)h{5fO+8<#aRqlMSB!D}o#s;5HCMU|KfpSZr)G*(H*&QxQI
z7a~aR1ud*uxU@Hha@mzXXTN_6{j5k^_zak{)G_oa^i?5(e(RP{2B9L0Z{U?ANeB`|
zoOrw5La8Dtlroi5@hWQ{U|xKXD!$w17u&phFt#2w;DrYkKpb`U(q-F9?zW|;!!l(a
zvjG<(xnZ|(BFl@FZ6R@i#u)AKhV$=le&*%fEkh$PDad(yS)|EMhP^sfijMzE=Q76;
zlS^z8u#sEy2F)X81=}$*rLvApnW^WIUuU4u4h0lyL@CRCV^(M4$-CCpe4mx#g<#WK
z^^ZqiBpRpe1T}Z0M)@$mp)a5x>oXmjxeBasZvrFm-!6!y+#qu2Ys5-S@J_qOF`f@_
zA(*>375d0p)YIKoYz-t;ynsm>xw?j}vDn<UKcaq@mwJg-OK<qd-#@@#yvctWYD@8^
z4S)7534-jyCzE+>4)!*BQuJ9dtd+cM5~s?pwmMeS;o<R3eO$_+<l%V^vA2fQH{9Ij
z+Mgfc*KfA6cdwa%Xxb~6QUmW&6<u|jPA@%Z-#)%+0<s7RO};He#S7lfWfg`G{_(=g
zx@cjzne76LY~DZl&7U^5jaa+M2a&L2)|9J~W$Q_P#zrH;C}$ToFe9xt;IW=0Y+Fev
zIq>dOyYPBpehCaZ0vUC_*zKAK#U_hQ)VZ0%k<9Z8nbJ<--QD4Zg^#~}T@#fCe1C!c
z93D7Rxi@aetq%JwNPrlGO=U5`+)6cyW5p^~&pTF>VAAKT)X|lqva;}9!WTY1hLXmL
z!on*&GpO5di=~{x5$nNDT`}&>4f8$yVpnms_qYHT`(FDUpI4J2B2u^6U!GPTmU2qn
zQo1|+!dftHl4EMM*1IjQJgU4;cFiFXinx2X-ZG$~Y;d@r3sN}H9PFe_nhrq?|6F2I
zkByPqTKu)+E4ZY|q^m1rTW!!bI2<qEu>NFM`4&`nN+Q^M{GL>7u>h+u1A~`b24Q#@
zc?VuU!PK<%UJh`#Fxj?rUnk&>MWrX0Qkf4nxlBT-{@zzCVC)j*<@ClS{iiS^y{S(U
zUg`uQId!f>Y%UjYyZDSc$6NNXD@ZNX=P;$*7JBpnUgPAr;NZCMe6=ViClK)8OAU{G
z0k>TBML1eHI$Gs^oP_3UkM^5l0Vn5^7#<d>^S`|iT*nk4DkrC7Z}Q7az}n7Y5UVqo
zq_%};Oi=_UKGdo6<8Zq5G<76!f?5vv<ZWiqF`K>IHy;T2sY25-DM`udeTQ8_hTA=f
zUAuzpbHJVBr(CVeywvWx-remXWK4{G9=GY&bbDiX?Q8AE$H^wzu9zf@D_*pq$j#Y#
zGYx!3<dN(9kDa`1#Ivi4#=gC|-xxI94BQfGK2@UcyfwUbUaqnRmS6f~s@~79s$z91
zPs%EIJI?IJhf{z_C-91ff<`3wrxTVFSTllm=a&-Bz>&i2Z|`OQd*J?Ocqd)gT9Nb2
z$;r=eHW5!<PiY=Ht-rU3adKyw64e0!_q*n&`23xGs{+LHb@FpA#f??b0pHpeu(IMV
zE(#*0N7B=t&bsIU>(CJV)D(a3O<=`FOX&E#NAwF0!Dd_~a%j&?9c?<MNIcPm%gnCN
zd&nBkc)reQ@o+$64wP>2@7!~GJ7ao#ClOZC<a=+dn1b&P(My-%mpUl|fcLX8oDsCi
zcd^Qn(oi70EBjzAtoQoZdDPJH`1mzW#n#9u@j!)bOH6E+L0&WBqN)cFsHc`<R#`^h
zlJ1t}O@2w*_g_|6Zip<u3Pqj1#5=(`Fk8HidwQ;X=!+EI*L=*6HtP41pCW6pj7oo=
zm8U;@y&L+LaUz9ETp;d;zxYOlv}s~#Y3b(XhGgz&Z-1q5Lgc9{Xzb3(<nA1;1Ss^<
zovF}`yPtNpg*pAFskSs8tHm)+-(hHlJ&%dulv*enC1xp*;laTv#l0%8dD-4qo&AY3
z3^K1CU)o3?QaoD7r%VZ*M7S@rxu3w)`^0o56d>5S{b{_=XIO*l5yZzsLv8hRkE(`8
zlkwlcp?f52%9b)$WE2~5qif4spN1yZMl5M_lRZyreCfoP;;}+h<+TRC^_e4ddR}#J
zUM7SZ-F{GxM&m1pAUWZ<esp5;XsrcDjg7$<lwW!byR5!oQWj-!K0?gOwea1$Eu5*3
zkFE)r_vfM^WM>=6&L&T2U}RQPWAv75h>x~0x?`|h-q0&+Y?)xqLJy}h5YkRwHLY@v
z4Rskf0VeIdu|Dv`iietg$FaDn{LEdj>*~%#!2LWuEqeNvzEIXSvz}acs+jRqtG9@U
zk~g=c2y6R9tpwwd5u>>1WaNkBXbx>-yqUuSi<^*t>x078uU-vV+A-SjI@$g8T<Zfb
zdFoul9Ri~Xw8$*sEC<KvK{tgI+j3s<r#R*1wFk2zp-jXNbX`(c_57Swg%KMa1JZ8Y
zm`cICc}Fu$hfUyYZKUh)n8_-pqO`tVKorj$yz@dXVAHaE&{OJbIm@JpVAT~jU2oIM
z;}N^lB)SWEQaUnmvQ~S09lEke$h@m_otbZ$$U7*X!Z<21@W+SS4<5whOU7#@yBD*~
z;dL9<6mUmYTZXKc?Jl8FPxqb!uX?)>sz1YgxWVsartPvTBn`=?wCAz*kg7%pNkAa`
z1~*S)j`h3NwkE-tV*(|_hF;_<c+K<@8u3@yKeF@Q)eu1Si^`43H`Y+hX?4&b*yfh<
zW+3wPsRd&b>%gWSC$fGBEj2Cbah%thML&6~3*wgMLC!pW`XIJ5;GxZ_Fx2dJ;L3`)
zMYAk|&;>>B>@eu+RzWw&dOSsZY+70^n$Vq&Bx06Qli8T&^|<4$unW>~i;#oJQ6h1@
z<kTrRIGEk^7zR{a#VwKqb{Spdq&lkxdFUegY6^f%i3^8H>~t9L<Wrc6Bq-Xf0wTwL
zrHNeq`ZY{&WPDW$=TYknpmo1-rV+I7n@rEf1hSyG>Tx$U%CMrO&cOV((8Uv6oY)3G
ze+P%6t1G8DoSiQw!IZf4*^M<IHunCjKPG3Igk6Mnce!7sbzU4HyWSGI*o#cL>Yi!s
zKAF5Zq`jLJw0R>h!9>0&2Eg0K#DFcB&VE{W3Zdoa_XvGCd`7|Xmo)!dF8)dT|4@*L
zP)(VTy>wW<e%3kHYNw2TT(T$@jksh=3*i17E=Cx&)A+fIP}oOK_rml$9JqEMxo))b
z#$LuPB*$JjJ>|JYz|yT`(2c49s2KlU!?VY$t3CF9UBK=%b{`W7JAPbHaO1)S=A}$(
zV*ofW^C|JoWxwc$cl22QwWR$k8~<JS{`0IKe3r@80b3h=Nc|IRqZ+<7XtXpcr@d$G
z^p!&mLMAQr@k5wbq;!B^q*1x;dESTUUO9E(JMiI&+H8Ymt;b!E;)6!Y!ERk$9bSaA
zw^ae1Pld#)#YOj6g^=f$mzPJ0^6X5zuWkiNF4Q1G5T%Q+N$_)e7Mf_9#+;lLC^UZ{
zJpfANmMb!^5nKIGN-*xd)zqvsK0ItcdNcVt<c@#Sq=UF9+t%=_QRa-vpg_G6*@f5~
z%OM{vz7amBOu4u7i;47w{Y&0VY2bJJ;4X^)c)G2P%1m%8R!5UO=(!c4B5(kI#yw+T
zzBWE9J3pvMR~Tlv*y%2GOj9lEY{t$OdZ-Nr0Or#;df{nlR+^m6bWf++FBkgt)kvJ^
zQfildJY~(VMc!*chjOrQu3RbK0OR8Vhh8@Q@-cun2}b6cU*V)VJ0!=NmDy|Dm9VXQ
zCbG~-sD<3;E@n~tnP4Y4hHlVSh~|4BG&G)l^1K)cO7|`kAiJs{!u{;-!1rFwk}-LV
z6{aimC2a1E8<U9j?W%c7bGfSEh}0ET;)~C7iz^ya?1Tkm+oS@y{}bfg&u7c<P0iBg
zr>D;eq5|vfyqQm_7H%UWeZJ$Y?>TSgqTD{qcb3^XjErmtI+Z?SVU9h&@#ENpfq)vs
zMuegol29Y)b|Y<4GA4<mpxAwG;`Ku5sJqZ8z}K!VA-DhF;R_e!%dHKSCk*ZZcjabY
zd2i^AT7tKJcF4h&=!FY;KKhSZ0N=GA%u$QFB08k_bcdXr<&@t4*~c47YdrS#D`|d5
z92<0x#M`zd1>p8(0e!wsCjIE`;Od?3Fbh33E#K!uQwKZ|uty_Jdz(ED4i2&V+hwGW
zB-Wb3dri|N{FK1y(Ia~NwoGci4T^+j)0(~sbqL(ZI&{JkP0eWcRN_E6Y=n=GPZ0G+
zPpzY~JvTSE+R7szCurojV_N#+84pW1Muv}K+jNhMf0^oE6WE!XO{m~)qx&i<s6ImB
zDm*K|akD$=i#_pp0w6-j`9BK)$iY@XFcV5r<kX}u#=n$J<x>X!<}JPcIG!dN;*!VL
z^=5e$kBHBY0UT+4&M@^Uz)7=&=kc!hR}Me^ar^*~b`34`UQlxC_n0tv9|_2`U;q4&
zt&i#d|CVKck%*IC7RTU~DiHgRwm&`iR8Pku<@UL<Y`=3k^U`@BVZ$`-_U>%cy-b+%
zX1?V3ty0CVi?HHx0X0<SlU0Nb3fjs|*98_OC<$ipGqC{RJ6g2sy0tI|5ZEH;O`X7<
z%TTq>cPr{{vSldpSRW89^T4hbz{~Zb=6ctpDR+q6j&te%0c}o)rJNDBZr&3QB}Yw6
zT3JJ`U30}&yS;x%m8(npzT1B?4xpWvDJjxFTf)`bH7Y9{*N2+UiCJ*7gYJBvpJ(LQ
zv1Vb}z!zc~`~(NsIOtI+EkVvb8RiOk3iUY9$@80A6kHQAw|S#8uE-qcuTWRtb^L@1
z2?<3;Dv8Q%;|x#{+CI$G+!DV<5v3Yy6$1#O5tEXjy^Tf^>3DqvJt%t<2@TMzJCsGt
zNvCK(tD#VsCImB=j7M4zYf}1NL1bh?UmxS|sh8zFCpA%q2O8vhI;xZBe<>ftQUzFB
z`<M2S84uK;KL)6sfJ_C{Fv+A#el><*lFTXIWH5o5VRAZnkSpI`^2~79h!mt0YOKmY
zso;rmHMOwH)DQ%R>=iI+(3Ny2CUdrIxo1HviZxS&VS?5nA)S*=6s7w^`4vvesj^$K
z@EYqZN9)_S&!u6Gy@J)*{oqK=lj<UHxfoOvOx9j}Lnq4Z><q4+D^G&WrNp+750K{K
zNC_L&-fhVP_8ptS4{bgX^2%3rW<w$E@r+Rob1@%MQ}eoF@a`)D7v=rb1yM1a!HV*`
zw7?NIdfc1I2Rl2FiioquCg)J7{cQcL+fD-^S8ZD#zIwH?FZ&bVgb3y_AMzCU4;me`
zPSb<s>@Fs9#b&lHGq_;kHwr!TO%~0n4{Co#I2+XBIkqVt+492$x;XvY0;Jq_=Zy%?
zEvNY#%x=zbV_tOyg}d!-qQq;`(m|w|ajGNmR0y63!J@1mr-)}QuWxm3T3QF)4)U?1
zt9&TP3X(7gInc0j_fl;gUtWH*zQ)jzQXv-wqk0HQmrwCJ*elaTHn+Tx;h71E-lB>8
zER;mYr1Tm=<MuK%D~S9w?Wfk#K%P>GAEzlD=H8du2il#{=AQG42%^{s_=VV~Pc1Eb
zm#hMJa&TGtc#i}?-#j`(*Szta&DRNW4l!&rtfsD>26@SPvz~WXV>@(KLtg-u%b1pn
zI21&;L<iX174Fy65ED&JOjtYz*y7g?_TOgu&uT!?_rDw^S7-qlLU)p|Nq$m&UTHdz
zURT9eEhP*Aj@!e-mOmfxBrn<+$jnDZ)pPUoH$xL{1!yRO-qZXur~g^<(m81b6Dc0V
zE*doVHUc#tZ!I%jvm;YSd7^<5mfhPioIz@8Kt0{k%kuKH@bCpaH&wLvs^%w_tbvqj
z9$g~0B`ZE=R8h5*2dHLz*L*&J)7HkmM#L3I#;lFke7q&Zf%RAqcgw5p@Qoc&)Jze<
z))nTKsT0q92nWD0oRJ8}`U*j+8`f0n?J?yUU~qKCw=md}=>S|2ccp(sQO%@@M2=E3
zQsXGO;RK+`5~cz>UiZ8{Z!!Oz^<Lw<clid$|Dz5zd+R|nA;{KYX12G3sbOv{tf6b0
zEAI~twuN(HU=Thh-tR55>Nk}k0k@zqNoO0XssS1GM#n5rAOl2WRxCf0g*s3=tgc4a
zl4h4j%<}oz66wWyLavz;kCh4l<su9w*4Ov+UsMzAvSES(0s?}9X!Hzk?ZypSTH2=?
z^gRQKfEobGk%gVACZVFHrLSviYt3umhnOj1S~@)*;}wD6GG_3JrH<lZGq%f~GJN^+
zWg_hPb1DiW&B>I+#GLMtSUQR+k-L<=+!lORh!xqFo9HRSez?O|SIE49Sf2Jjegs{A
z{r11C&dTvCD2$&aofW;4vnzh}7{GGJ(XOV8NBE9(BnldYY$jwaX1>ve85sD)o=gX*
zDohU|kktP`E@Q4UT3cTqNEJmQ0N2rUc#_icAL_wkg3XturTwOwgEuxd@Zv6TINa6s
zn$u-d8q7nM^1+KJ&rd)$<>l$QXBM#dIon0?Fg<>M40A6UR(Dxaa&T_Lb+WN;-@zbP
zM@vgf@_#RU-ZM|nz_9W|xp4ySCr8$15CypEqq<A_JG#FwQmf7jNef0tM*}&oRil3y
z;E&&n8`jcf9=ur-e9Q=_^|<b%s3BRsJTE}r?Go3=6hDr5$*_y1MDa5{0QOfEVoQYL
z3{6Z{ekC$CmvhQL{1@CUMqaHL0Ic=VrxFIrvZ@fEf+M!!uK-x`hrr@tE4nR|a`Wa*
z8Fr>W)InVI=wGn=zYaa_0$|7Wz^v5f(VDHT5a6V<nCX?UCw=;%J6~qnB5GP3cYZD{
zoH(Kl#O|e6j8H!R%Ek&}^X^*1N^yht0JY2EcqXIO0rlTsTWt>MRLR)NcA%7$ln=A#
zwx^fZVZi7Uxeo*U_jBcxmjjgoK~d2|xbT^6KR&@r!v>gR{}v3Le~C8815$t#z@{v3
zV1pPg<%8)b%vUa7UgW&|6^QuX=l5P26}@!n5+9!$k=tazvBL6zp9XME;Kv7lQ3Yq@
zUp6T;-RKrBk;zb2s2p1Xhn_d3KXfb>foqA~bzZnD`kCyfPj5Zhb#Zo{4B2(t!aef&
z^|42)IKB>Ce+IU~N#Dq5gi(52B4E=#I)Nslvr`>4jC60V^IM-JnDnQCduBst>~EX}
zw%u^OC(K$hhK!Gw^j-Z*b>wK!<|lsZppA}F+cs~;)9kISt?W!)1U%Mn_3PjaRG2cQ
zc}S(_Sq8$ZVS-{}z6}%7Q$ZCl=bwv%Ss^=uGmCEq-)cyM!AqH{Ak0Z1VZEuq_O19J
zzp!w1q`;&n3$eXyWMtHlH<1k_k}T!6!ODBOsODxRNy)Ot#=UPG<+-_zqlISM+uLF(
z1@oLKJ@eavPv-d1+yIJ&xlWgJB}ZcMnbPi7W@eZw`R{;bNibVmTT%XJi7>$RAjqQa
zj>n~E4j<`A%Knd*h(1Te&Qe~<5>G)vK~z-K+c$3%IQ4rJIb->Sgd+7DDrA07y)R5A
zkx2FR^?Q4JK$vjJdfNY({vb+3C}gg#x^CgnLc(67BdMVlmA?!z&8mi#Ve$9x-$xKu
z0To3At~)L<(a_quBys0^f_`TVhs%KiQ2_j*KVsCB`u9=gtYcQOHR}L6gnHnx?ky8F
z?$%oopUj#Y(eFO)&Arh*jP~%3`vOTkH^SNFeOFtbGAP$lfS0=s?aNe@7ZK^*Ln~1B
zr%+Q(#tfDKgvCW)x2@<mnk+Cbx>IhiWoem_?6KDpx|27Qp57J938s8rJo)R};Kqx`
z{*R15=)Du@2Luc@G}6NNEqH{fX=vja1A(_5OadYdRJb;xEx`^&Z|Ez6?eKR#aHyUG
zZmzyu1x*7o@%PUP3!9<*V1~)FD|qD&7rzF|!z`AV*M`&&E6i(F)T7f9Gm8-?O__cT
zPv2Dhx0cnPEZ@f0F=o-<8EvZ=C^NoRFnPnk($c^(V_LKH81TVINJi-VxBP;4q%Y%j
zmQ(tl;(0Bnjvped=5;5aYu47Dm!%gp{itAa4{ug6n~*^JJ3fwo2FfIk&p2fyl=$ZJ
zrTuCreEBJ;$EN{&1oa*Li~Q+VPp}r=F77f~DC;qO9m%Xn_-gkhS63?FP(3}2|J-{N
zHJbvY^~I4<F2NLBM+X3|Eu%B{01#fB{?OYIh4S^^;_$Pe%yDVsMGvFqcpqRyNEya;
zOhc`znSx|Ex2Y>r|0O_4TDsx&b?1oUA0C-9IY2c3nwYU*uv{!^KB}8~wbn`BE2j2!
z?bq}p*-?K|7rFA?;y|7rhnVQdKe(%)MUFqOQ2`M7xF?dI0q6kmUtM!gd*^L_Y3b%F
zhIp{Sg$=4)UAztUFNHZzevF5rV>equ)qZ~Lj9%wZa;-FXzwrc?zk_vu+V%ALFDDxn
zNYZ{o$0VZclYdFPq)&q_x+VEFVK3lqQ6j8)!4Y+4%Ae))pEK96wPhI^(vyJ&gE!_v
zHlj4L0y-B5>mwsangX}kuf5Z5QxQH4y0_qeQ5`tLy}K2dh2Xu7d8D14U1&;1QKC>m
zQPX-g_GcgM{^7YDAp)!|t`qfD{nOAFA3tg)L_9+MzxxU~&V2Yc_D7HFp5qg*ziW@~
zJA`+prPW8$PZ$J=7iusgGqU(afaZkeL&qnuy6PaS64>$_pSF@!`Awq86dR?$y3e#m
zk9Z~<D5(ANv%2b51d&rYG{n@qQuvZ8Q6%Lnd&~zZr{zp)`y=7ha%_p+VCgw!ioqW$
z3vgR21=_!7qkpBq|DZn(dl;Rn)<Z^CR>g^T>b=ozGoKZ;;~Mq}*gU<Ad_<%kH(M@1
zfU`~z5knz(4R*$(k?_r>p6+-E3k%Dm?RFK&VRNH>!1Zg8Qr7V=Ado5*?!S~+e{I%*
a@|u{$E5S3zm4H4!NJ~xcX0fWx<NpEMj6w<k

literal 8327
zcmbVSXFyZkmJJGmNL2ypA}YO!fIt8Rq<4adG!+Ety@e)SDS}d^BQ>FED4_&`Km?>j
zdhbno2~Aq&qTkG$@;&Fx@Qd7Ya?ZK??7i38Yv+xYh9WsB11SguB3D+D*8zdfF@Zn?
zF(l`JC)OAEX+WUsAZ7Un5YN=Lac{@I-8%dhR?J&jmfz@d!hLzdcaF-hsB)+|wUj|T
zM7d$O^EqonP;hG3W4Mv5HeuSwOy+yp!l!-Qt~t8*TUZ*ho!`GEA>@j=ewpf9E=O>%
zQQLd(A@luXYPIgUl+O9sjm6qpYzu4J>bj-OByw}PzSVF4qZgQk0Q8FN0h|~FI-pb`
z0$nH1JqL;j)gb^W$-zLNoGb_k)T6}>0$Fj=fL`5=BL&@O_?u~;;Vjo*@tW4-qr~1S
z$`cl{$b(OI&aVup>q-%wzOlWJ-9BlbymzV~?-;!Npt+Y4TxUNbQQFQ)GkaIGCM6lH
zDg7Y_N+o1BLe<YcCE0pm=WY#S3Rqq9wiN8_u~OJ+#RJ$i4vCt?JgXGZ+yWNDJUP)!
zjvD=P;Iob>j3p=gUjCmBj>@TWK_Ir*+*P$=211TZ&?bDoEJ?(}uhNT-d22B&Id1c;
zTZ4tAsu}r;+T3YcIy%B`%cA|d4UxcM;`-v$#zpmZuYS#fNUZ6jRZ^wAJ?YjDPLC|{
zhl36|*z>sSjNfsE&8D3!(zTa7eDJGB{wE8iJ&Q}?aVq)hNrH~kjorpoX7=_MDVa{A
z0DA-nT%mnyG87`YkT7@n2<G^a<qxL!RQ~J)hueFBpW_yIE6g7Aj--k=&CW7gw=|>y
z$AgT+w@I)IMV;0ypI#=2H!U_x&eWCUKq7T@bk?>!2a4JtQm;8V3r1=xcs813DcKmm
z>*^TK03+rl+Q3Kw_mG5l;oyt7aHrGbMIyt>j>=(PI5BmdH*p~g!Q=zc%th>_Q`Cz+
z+7wJ4l&V{@%0n?hn>*C`ULzzL6nlg5`z#4Am*b|mHs$}rb^fV`nfA;xHa42{-0iea
z#6`cFZ;u@;&ES8*!>I_|{A#YCdhhB3cdlAKO_O@RL+F_^O={^cCWE~;`(Pfb!)srN
z!&HWeE$)kE=6C6dd2P<YJT&7Gqd{`4tF3obFqSzvWTT&+g)VbFRWLsf)d|hDP5S($
zmEBq6pG3jta%p9ngq!ctUhme{$p#7mhd&_E)?d`QdsQs}xKh|ker3i4%cRU{7f&Gr
zJebO@MB<?weUy&Xs0-Hjw2gyq6ty&iVf@;mW#Glb!!tSkqu=K<tj(;$saqOBAO*}B
z<DiqV!sSJXjdVr2#v{4Qw#%66m^$fzQ25G(B+BinY;I19jBLkX3fEDH@^VrB_1({A
z#MgwIvZL1}9H&?(O}5P~=@?v$%A;-XYd%+d{&hZbMi1j*V(`R}VIMj+L|_*6VY=Hm
zn&qG+V3ZDgqgHS<X|^&GGSZ85XicLt=9iQ7?<@FW)>5)IUaLeRWHaz~Yt}3hEHMID
zJ>NlTQc|EMnao$m6|z%cHu!eUxLhBY)Kau1G#dr3$%J(9-W#&6xR9GeW>fzXY1r5G
zD>Sayl2=|Z&<)MKYg%qN=d-Ebvb8MmhjcQ13nR_W!{ZOQJC|YS2VtMFdqER<#OGtk
zf3$tWj-*x?e0$^)ilrBOntJB84kV<c-#Sq5KX^U-W{<)210I}!powE={C?%?)i|$P
z!Z?+@xbg792xP~^j2nIK45PKp;6PuimuU&+<3oiDs>7te+{E3^E~-%B+aub}%k)gc
z@8W@#KaKLCY#8hSA2&k|c_~VP8p5_x!q3su<A**?;|@F(kJ{fd*SfDHbh8?gR{+6i
ze#~yxw8%KaytO7E>Ap5poM-qovhTLa!+<nNER$5S|GE(@uL4<AQu6t8w_Tr>AQ5o&
zlGs&nvj2|JlDK*~-P@Y4H3}Zt&vYvkV4Q-^=5bUXGp9b7)Y-1_8h*ZUlIGzY$v~P1
zxV5EupAwt=7h$40+qw~h${W5IN%4(qA`r$ur^0`h!+!<hX2AOew*@sPJv}+JpL4zG
zp@yc^ZV;VG5}U8#wNSvzKg<a0k?Wm^?#I^SbY(o3L+AxOjTK-?gQfny=uQh|rOoYr
z2IH7y3AMv?!OK8?HJ!xUq+k-Jlw#^#mOu5q<;{k4th`fHklt=p`YXSJ?`)qv_~;1g
z`WwtiE!ZGLj<N@P?vJMi5#y1PM@Cgzw=J(HT^N4Ff^6Xn_7qzj55jwY0tPs1uUlra
zD8O80J*(<GHl{v)WXLbel03SXwmUN##&$pq7<+nebK*-~gmri-dDr^tY>`K}1JAb(
z&Ug(HN~C0(O${2$Q)-@@`{DwT)%YaoZ6N(|jIpd6^%hH5?Wqj#Sbea1kUWevNb;2i
zy`tPIoP;bdFFz`NGVffyLp!v#muTuI4hE04!k%6*KQ9<+8n5#3A!ee^l0(C&7<rw;
zazz*$x7|Sfs`bKCGBh_0o4liA#*ZJLp~%qSR(y=e0V#su+AEhc#67NufRFZ0nwL;H
zP_iUdlL@@f=9e9rlcoA-8IvEbCJ-r#DVgJH2<fG0CW&%H&RpE`gQxs%Zn?yi{F)km
zr=MG#pFh9tyElBN{|dorQ-*3T3Or~{UhzaukMf)g7gyWca0V&QO|=xh8$w%18XA9x
zmsKz*XM^TJ&zr;d@1LX;*U_T9aFPxd8cL6E2e-D5;_F0cXm(Aa^-L#+a_O@a@)1HW
zzeB>zW{@5oZ(d(xVq)TI4b9+&@qH#5jue07o4tR0AeF%tUtvRuI^KTfPzYbI8*C46
zZWasqG5U_(+HWUs!DUg!)MrcU`ExZK#-ME7?&mP2t0<$WVO1wBe=vuDz{!tp%X~F2
z0}}NZa<*Xni`j;eL`t;n9JR=_%=A5d=sHGD;P%&>qNb^C8$}5jqtn8<J!t;|s+oR$
zU3T`M-GO^)xejRG>Jwj4`&4>nsn(V0y>+RK^z|1!tlJ|t{-br09{cNK3lX`wBBwhI
z-66Jj??RZQQSh1?K@m5@_La!C&`q>$@E)BkD*4db+%bnBY}DJ&;c(vdJcW7W;OXAT
z`q+4_i-(vgZ!y<yq0U9}ii>Os{LGA3vXA!48yg#ulY0p43}#C%jA9pBRjBV^VQ#cE
z7r7u}5h+Ka{isrc`x_-z&`p$4T^%WX;@W2H(U~NU<5MpyFJfbaTfP(MqvZ~MEa7gY
zRz<DuwY$(C$wPmEsr8x}lUXp;i^BGgve^=T0vTL1_Y+X46MGL`qp|nP%Z&>*jZJm<
zz;l`GoHT@~2*enpSl8Ob$^CW_)kMEyN0x?+1AiE=iI2`MiD05~?0`mc`J>&dul%<c
z_kk!RThK?t9v2VH%*3vt9@G@AmUmiw=NWj${oAR-o2IMW`3BbpPHH+cGczaZycxwW
zs|DJEzHS!kP|I#sfuw+muh8+~npN(_IwV3K>lzW5OtHy@MSW7X<Ye$yCJJK(fLT15
z7h!82OLO7#KvlyP=k*sZu_c4m(`x8)KQ{d6ep^uR{o6N*XMG$JeFHVYR4kN~OcnqV
zS(cl*LS8~%80S7?CDdJk)1+Z90AE17P;O7SMeo%-Xex7>GU;PovHe`848VahUaMim
zO*wSl^zLjaexY~ragc=mm75p;K)QbOU6uRy{Oi?7sF_c~^Xi^f)K}S$FTyzj4FDt(
zH+455p*~S5-wU+x?XFqJxiMGMIrx#0ppRe7U?S$P+$OWFKlm=!)c+d<aqZ2fCcNl-
z&!&PGA}GoI3)uHRLe9zR^fc`3WWdtTS;zyK#_FlgA+|@-TOj@P-2aV&|5G0Ii_i-!
z-KmiB?%Ei3dDd6(vU)TxhfGz4fztz<zPXU%kY}e+rZ`ep63N07%2A)}D=5j&-}UNC
z$MuG??$zcuS7eg+v$YfpCISz)p<50L8s?<Gm%<kO&~`?u(<i*YE7-OIkg7gWd$7;8
zdDf1desS{Z6-uW5{{A+`_Zu43wd@hmb&f@qm6iF5ccMX9g|g)2<f>avSJFRZBBy3U
zSoI^U*%j{uMTLo_^Mbj2NA+U$wYjAo#;OPaMAt8sE{0MiQ2==2bp9)iKAoxWA^d%|
z%U@hAW1jlR4}tY+gFz{hF2b~;^3hYVq|sMR4og*U<*Ps_&s|}ov1oAM-c+8io*&RE
z6p8bvna)rOp-)=T#8dhoH1!wio0*vzPP%f|>fB5h@w=I%+lU}!lb<*R_Xjn|k7!_E
z@*=&2+%ECoHvI8NDPj(lzJ@&@A@tA^_gm`euM|WLiEC*asOj+OXHA?7(8HB<?{%-8
zZbd1(pLhp*D%qVS#yqG(fs^~u@V-Lb{zSq4Y5mFu+%h0~$!wz#8Vq_~G70Hm7uc{c
z%a#;z3mXyYO5-UmvDcCeQjYZU=}2m6DM*(kK@j+QiQyQ=qhOLc{coL0c8uJD5J;co
z6)_r|l9D4C!__P(X%aPHCql)>%-0X#`C5^akdaF0Zd`w1KCl9KtGRw>ryZW(-~srs
zfz*rLWv)U!O}6x*eR&|I=_%$zrkZFojEbOyNfa=x2%P{}wY3qsn564MCM*k<9~N*?
zq+hHemP#|WrS;i$PMW0QgRR+Uv@h!PX&u##S!abLDckL-w&FzNlB!e}DNB<vR8rEl
zCd*(Ik4fMC*FDs%C#&prwqzA!rsl_w1EO>SymE8S{_f(zr=43(hZNp;eBC5;IE7>K
zI64|XTTJ7C3D)Hfcro<p*#;W#=RNF+n*&hR_V{T)q`p7Fe=bt*<v+JJ^*4T>VG6Sn
zXdU14K&Kq`s0z=oUkrLj{^MuO+{*DcpEV-&^-5r%HqoMf4xoe2tqUKiPgL;i*B>1!
zkM%ykm@FfsF%zm42+$pPTcP{>dQIu1@8$h+LW6~t&W%<Tz|U#<nd%&;U;ag4c+Wok
z2!X%t68}?`{O1t;o0|LJJ^u!UvDD7jH)5B~F6&X==<LW6=AcL}fRg$H1aR?tR-psR
z>4uPy!tV8+j#P2indS#3iQ3!~b|=m&={Rrq#q~#0ukTvv_IOUkoW0IKvFZA-i{Jjb
zQGbw9Y=UTr&O5W!SD%mgS8bs6%DdMEnE`@i)<Q9a+>q7n#leY%7#9CV0YFP=o0^!M
zPKU9&JATfy!Yy<%3O>Cb{g$v{&T}lLy;NoXM|XD0o?Unv?dUtq!<O(HH*V1KJ?ZP!
zB@isjR*beEDHjlRf1*fBN5eepl<n)M$1O|JLfF#UqTp_x+p@N_^bB-B7-rVk`YzfH
zcrd%Z^vs9(*GUL<V4ltO8LKWP&hYf}uN+$2k1{BwlTPzx#`m{cE~Rxvz+1M+19Z4U
z6iF$I!4PM-{O)y-kDRgb(wCt2*w_sJ)z7I(Ny-_%m1?{4^=w)yxnSfNgLOsd;i&jc
zkW^02O-XL+ovAOvc9pN2n<pPZj_b0f^Om!G?q`BqZ}X~B$<D1|b)`r^lY(d5XLirh
zCLwN4UY?AC;w?n-z2@czo$49XjbJ4|j^WGZ-G;g;hLSfelv?(U>ivI~-NHhRA8DIT
zZ*A%b;g*#|p(MkC)jayCvajdnJa}oxEnisMxP*~e&7NPjt8`4^Ga}J6F*)qc#%g@n
zMo=YFJ^#6Vf|Xu5d9xE9e%R0vijDi$)Wq6_N);D!|9Jauoru>9FAb+7@bU1PWtnLk
zt?bQGO_t9u<x^I!FkRfIs2yC%(xgoX>-ob~b(=_-+Y|sb;P(DzQ<Jc;fM)8o!X-s^
zfzpnjYwaFg>Er2XC*f2##Jx^lQ%5i`a8t0F=ouR)CD-stKy7i!!GtY!`xH3nk64aN
znrZNjQ~yBh)(4#re%PH<f2@^%r($}vX!_95F%HOGKnhbkTFFS-Z2nk1G1**xI(1kY
zUcWq*DrlmJ=$2~@ZBx(i)70ofBhd@l(O^cg^p~ezXGt&83-xm`FV8T;uV${K)}kZz
zXF}cyE^&$@J?YcSZllsL6ZGknzA25Hn<MLjFo1Om-`Ynv+{G{$K3ECAZT)TV*pWUY
zK!@O!Xk7gKM3s~M{yOoK5`&r@n-JVVcmsDlhJ&t<<-vz$<YmM30_BwVm0T}kN4%c0
zm}jfU-Y!nNYgN3=byZc(r*K{wRbI{o$WNYis!!upu3tiiwJ0=8?*`=uQwfK40d!m~
z7^u2EtE5ClXJGk$*MpP9U0y1#&*<lVw0bh#E$g8hCcRaBHy^@iy%P~~b(ygT$&cc<
zQ%MGRy97Zxxq2@^<!i>(nGKAdBxhSOLv42{eUC!>`a|+_)t3&8kKquDj-=0g=7x&;
zc%?Ca{E3t}1&CG9>}#amsH_C)SP^VrjxANW1qOp}VUBeDK;Hvf$g9uIm!UzR3z`2l
zkp0{~)`wM%@kei(n*ail5;ATeVZyp57f3CDwAM23><zvlj0<0WP?K9;zBf=zQ8!dW
zlshvH6o4$z9BztmV1%cq3;96ljK+0*cplvnn_MHedwraS-fE){s)DIyj$S{Q>*087
zLeU@O+FpYl?60xb)0}ny%H-9dtsfj2M$Y%3fOcm%P<(`{9O#GDYH?5OUR)}>>Gx)t
zt7fGFUH9m*-dVB(PL!{i5pzp*Mo+WbxU_B$+1Loz7!SF!`v+yRNj3aDCaQ*!D4xjX
z&fw!fUfk@0W_Vf-^hOd90FaDg%cP{-gGFuSj{_I5(J6Pi23CwY<L_$^KGuimmW$hz
zQ8mtPZ8ikZ0`k!EGDAeTwWvea<<8+u$oCsZZMOaF4LN58zopFZaINFts76BCu(`!W
zIy$<+fo<xsgZks+<3M4edHr^v{OV<6v@rXq?_X?GjVLJKym=GIQi5smJo*XDoRTzd
zDn&X{q-vqINl|b7bm_(HQ>ku9Pb{JXKs`~6Vj6J~tQ7dHGp8|cvQ>j{C+A&c<E4!_
zdjR|!{mH-%P8_flLtX})00i=3{#Pa49`UTKtmF;DI%vhRjFQY5AI(HO`$!qLL(`k5
zezX<sUjz-eS5{WmmJ0L-B#|rk09#13SXXEy-{s=tQ~wJ;2;#~A%wA1&d`2-5bkWR`
zqK;Dydx;_<BGpFxW(tAI03~5#EY{{m@;&}^T}%wg&g0_j4251xA_Z!FL^ngOv!Ra<
zs&{Fu%u@5HJx@I)Aui6mLrL%=09)qSA}aHuDV?-TOsl&B(wv;F*7KBnpMEdt^hbg9
z+`OJWqROZQsL+ZH$^bAOzvD20YK!G4OmCb77PweotHqsWR`Dd7RmSi5zzJ~YG|cnQ
z!?s{Yr86}$6Y&7%s^R8Vu}u9`2k@42+>EKZ|GR|lJPObl11+u0-<0k53#RlgxmFv&
z^Iy>ejODj6LPA0ecxnIQ8Zl7=f0W|?A{nQ%0B?WNQe;%Ev-?T#Dqy~);i;A2lTNJv
zDXu$P5s9`KC^Gm;c3u~dgV}``<HGST{VX>${SSM+a0{?>q6JyeOhu@u=i#M46iJ@S
zTXy!y(KUBV3kx_)&I-Q?iZgiA6AUNb5(Dhes$diM%`QGZJ}N2-27|$gmr5?t@fWas
zIWy|-cT>-hKG|97W%WA%9J*%x_$N*^kv}RTLRacF8aSDp=#y-S{iTZ+FJ8K&s-mJJ
zr8H=jJg|+9d2M^2a`<J`KN3Kw^a-$$+gvMkogw;Q<`R2Y0PNQ;^_cHE!xc7zOTGC`
zO--Yy{&{D5aWb`#vjsN!6fz1t?lA$Pt{pCKWaLTEzkf?Q_?HF)sn4k@Dq7u~ZqfrJ
zu~4!P5^nHD<zqP<4zvNVc)*aOrs5v!MzQ#SSn_Hh9VlT#5jsw_<4a3RS2#3KD<!q{
z2Qv|+^@rAd1={e?Ey^!nzR*V8VrQRi2sm$|pZpUaWiBTHxNlEcRuLpTJbcyt=ruKa
zFx6~Jw2bo{$@GuBt=SeaQBioh>^TG*^RJ84a@WX3AP}Z#zfPI`mBCUtJY2I@PWUVc
znvU!7DJpVuay~vjUS3|BOhC!yzCKpXM~oP@?UWg{6$P$~75{$Q?CgFnJn=z8fE^Jp
z+Er9ly=R`%)6?_G5EBz4Q4M4B&Q{45726NY^MDK=W}AuG$4lQ;H~jqkAtiHBUf#mt
z?n<YOqP+aQw62AWG!096dBO~LOXuI~a`OBPI8Qt<IJh`JkNNsFUEIauU~{^2P%^D+
zb=7uu5ys6|F)+yJZ&dzk@uUod&P7sE6?JtfpM%XTxv)?&`aAYxRiU95*qZ4~eT1B5
z<YyPX<X;m9dh!%-{kqtN{OzUI(~~2C$DgLW^-t#o{Ff%t=&h!?64S}Yk6#`;b>IGF
zkvTPww>Dn_i2%!gWgYz4B9q{AWW?72w52GA1u5lJANH1yjg7^`#E3e~_bQyHKT9>!
zhGcy4ZYu*PGj!<hwQfgyYl~fJ!p^^1Mt_Y0J0o!@ODMGFT~h-DxcV6K$;K7hzweht
zElnK19vF*?Lc-zZYk3B|U*5e#xCcD}j0JfSq_ahka<m(Jje<>nyH^uCfp`d%AAo~K
z!-2db-9XF0z)UB0XnOi^Ahc<*<6Q+!ACP^sxq+ai{1h5Yc1_Y<<;gD+@q4*{1jXNI
zy#OkD8?ASxeW~*{T;1c}`2HBMmZ^Z#%_KtL#V0#2<o1*;^KeTWA##q6u4ah$o~S<s
zL?5V+1h5_T?b658Xiulajnl+x7vkHuRZ@u;0EM(gu?*<Xu{m!}1t=>U*Vkg~DG}RZ
z^BI6u4ql4h`>&0m>EXv4^*<L<fN-lb<fB!Ul?}u^7jph}fb>_u0cJv4X1z9n?ivM4
z5pv4aYKawpgpQ4kjY|Ec({scCn|X@y-f_nD!JtTcX|J9&cSdo_jv#=2HCUWkvm`mW
zF_uGku;^XI^y@Iz`lB$JxC+Lr|6#T7MFWg<0v3yl?IYi58NQtl^9LGuX9iWt_X<uz
zI!q2&^@i>*nRQU>)6&qpTz9<!5Qc^}z&7HFq?hn3J-NEKZv6(?GjQ0Hj_+#Y6QBg7
z)t^tv%7M%YKms)t{vETno|cx^+6XcJuynF^0yiGfe))1R)e&xc9ktz1<3^;dZD+qy
z@1{zk?R!##Qhs*#-+`>M6)0B(jNw(z^WKBrBSt62dPGDtfb8HEn-5ba`66a=@Q=9}
z>tn+UyDZU*bwfjY8<PH`l>l}jy>xvaVix>P4#}8D#(!o4;>j7p{I_~8Rd*>ocKqP2
z=7AWnHNksw6^x{%T+?*mxjI8!Av}`lLf+ZyJUugcmeoisRwg4KKT<!p)T{WG$!hL5
z^ai8?U#p#OPXzjfw;%qR{^bqye>Qlo>?%0+4-Du-3esmX0=@SK0uT0s&w_cY8*p@~
z_F4B!Y|@6cdu0_idf08vHuTBbYO$f7CiRaqM{*VAj8CUwpovHMcsZKq@bRkc@*=Hh
z+c(8sAesaS0%Peka+Tbc&QmNNB6UtJ9EhI{iy#h7f`6rh{V&$$Lfwh3@rj9-*Z_G)
zJOc9(N-MMfU5*k!G2`8<Y4=6R&X{V@u%I?<Xw5wWv%Oxs0cUB(0|@?e;5_lLAQ|9C
z6c%zgPw)k`^B@w!Gn(*qgq<AtNr3FxZvp;KUHAWXW;}5YwNOngtY8UP4W#@~L%u}z
HY2d#B7~+^Y

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 4e063ac96ef0e514f5609adf0dc556cd36183c49..5e22cd73820e9acbfe64b6be0f011a5d5ffe48c2 100644
GIT binary patch
literal 2607
zcmdVcc~nzZ9tZFsRXZXG0tF;!SS%__r~wlQVX?u0Adr?tLKPSb6i_5m7O{YeAOTHE
zMR7r>#wr91vb2UJKp_}4!5APAc6kW}6aq*Z)`Yos=Fj=F=Q#8E<DK98o_p?j=iT?a
z?^67I37T7WY=OaGnqHpxuVAnZa2QPO$4}Kk($(OV0D@?Lp8yYVtF~do26c7yPd0Ac
z^uedV7L9)Z8e28Av^2GKw6(Q$^bNKf80r}r8<^}e+=(#SWxB)E+}O;*#KLmt?mfFK
z_aYDoGhm;Mxi!+l#%?!q|K~{5=XNMdJJg;%d-ekMXe+?M(dvMcHGsz2+S(!kCl@<s
zS3767F94kTewTwN6v`fO^RRdKaBy%q0DMV6qtO_T!<a+fPM$}wSgbSP?S}(=h^~NN
zfE(Z+=;j}E5cvA&mjNU^9`6wp>PZUs0zxBve0+|CNBR9T#vk}LmKYfq5D*X;7#IY^
zojDr+eMm?Mi9`ww4gCg4Ja_EavExZU98XRUOUVdN$qY|D|8079R8&;-1<H58#k|-{
zSL5R1;we8RBqW@n-b?|mm!_tsrro@sSyF!CUd6@xm04L?mwtJY4Lq#QDXYDF`Eo8$
zUPqx&u0Cm^R<nQlt?k;=_QLv(>p;V^qN1W(Knw3y3;#CI+Ia_P6BHL0-{rji`MHSB
z6F=bhKNJi-dOcDG2uI7h-jsKbF@T;ih6t*tsHg;brImf-j{)%?OeV9Yrlz*Gwyv&@
z#bVXh*Ecpcvf1qB=H}Mc*0#2`7cXA$csxFzFAxZXLSc7zcTZ1`NF?g*?G=l~!^6X)
zqoZ%$ycruCgCIyEkw~S|@$vDAiHWJHsp;wInVA`xOg1|^J3l`!m&+9j#p2@P^78V^
z%8F8{RH;<!>+5OOauE!+Im-+09*|l*GaQpR9BINGL#U~_SNyD(LeyZLF5Jh0f;wWe
z8Ezf=?s$BpZpg*F`{%7<6E2+h)UNjU{gBRHo9{@gnZy!%LFFi6eUx86QSvTLt!24H
zikc{v@-0y6pP;&Tx;1j#Ews$Y+LSC$I37Z5-&}yn{pb;)O6D~7L~|PrYfAOSB}kQ6
zLBG8$2jleXpIs5GL?z1@n(U$T+DlMOcnW<#bvARg(H?4!NS&)&P*7KMf}T}RJv+N&
z{*mP?SCy=K^z}>3Zz}qnA>BE-Yuvo_z$UW%?U4748#j`v&Sq3w+}Y=RPKS9_?*Gy|
z_^=Rp5bJaXG=qL6m}S%xH1eR-_Uww0Gk%>olD{5zN~6MMH<jAcG5@l^zaO1Pw@e~C
zOWq|WqA7ICNb-=&suj}e?%sR}me3T_IhcW<mK1i7MPG#7J-3+OA-vXA8kCXtn%f~P
zsKGGnPezO>vRqB6R4}GrCwOg%ugk8KKafR^*Ah%JUfMvDUPO46W0I)4rRuL|S?ZHf
zXv)Y%S-Qib;S5t(YjAFkrR!2N+oMhxX;~;fB8ktXe;tZ6$-(x~8b2&#gY&eb<RuxM
zmVZKdDCisP)@>!pBO~N6{s@FgA5bUFbC$WII7JR-MK1O#qWv&n$Prc~BEd#8;P^fl
z(;%0cqI3;tO=chGgH6)ox~BM?6jw_M%9)d11TsA7EhAc$#6UT95#jGX3re56SN>|!
zGmJd+{%w0$LKcQ0*XJ&{F0^l}(j{DHLM+)$>}MHdHiq%NKDWqsxwUp=4Mz?rzj9&$
zi}vkq$oAVM&pw?#nGKbFWyCFf9J;h7J;fE2zIP$(P3@yr`9MqKzt0*F3YgGRe|PiR
zHCl5I?=YD7C<_ulYVI}e+HcZ9mS<NSx22kaO0dS^{V|crjvnw%6B6O8%g>vC{O{c@
ze4HLCGdb%HXE)4D-{KNVv<Z)HAP1U~r!~nvtDTS>XTKF)>Y%ugOCRxWc1&+E&e34*
zTy^6RtFkq9Es<0<f|_P?(lCd8S+?WcLHM5}vE9}|nsNGn%BS&0|1SOi3jQyy*A=Hm
z56rKe8dN!pi~>2tse*~(`q<9*0V#SqgkM_N(Gj9|DxAo~gF}qj&Yg$~Zt{d{-cEzN
z-oA5Zb)YtEH+9ny994g|;Ti96J}FniNJ$k4A1uZfKYYsM%nwcsBeb-htlyFtTdu@p
ztIyCR=3#o9H<Kt5ssoymrT&;h9`06dzp^fw6)2?)x^ks>eZJJSa;@rGu(hp<Jm7se
zmtI1fru;3t^;J&wX&&1gnM*%zOdd*B@FnJcpw=Z@ht-{(5gS8geRz0#!a~RiFl1z)
zTy<|KuurRfV=yfp0ZsP4$p4TBpW8O<ptyud`&G#jT7upUeR{>k^y4(^-||0GX{4O%
VM;FEj1mNTc^YZY;GY^Je{1>zCsM7!d

literal 2542
zcmd7UX;f2Z8UWxR)3HLKfJzXeAgdTw!xDi+5n^PK&7??ZScbCN7H$~`HUc6o5DK@-
z=0>0riV+bCh!XZPkyMt3J)s1m0i|q4%9spWGM_VNe$Agb?T_*K_1*W}_dDOY?|HxX
zG6MXF8fyA#2n0gI>x^d*0<jB)K&V`OUll|~+q{xMfE?gUB7jGgUAuOvs;d6!z4!k7
z*86~(`W`_219eSJ4J~agEiG+eKT-!k>g_vVpsTBkJZN~p@UXtVzJamnK~oDu3riy-
zBV%J@6Tr&W)Y{GrusvpOi?Oi7SON~tXeSpdz}eN>+S<m(#?}RI=XTN_z`0{E7>APt
z2X}&_qoWhxL3DO@#sUOy7Z(>-z}wHw#~<e#h{xkk0RE(tKmgg@-QB~(!_(7~0DKhc
z1%yWW`ud)Yi1GhRd;suCLSXcTpqS4{BodiS4hadNP$;3Hp&tXubSjk^mYN<;%ZQ+5
zMx<T-B>n4{n3&isMqFH60`OJgg$oxxXA~vo7bhhpeF5J{Nl8gfO{D=P6|~aIw6wG@
zZ&cCg^o$C2X2reB-_>T_xqqdqE;~E>tM7mK8mMW^VK?XI=H>zS9y0Df%74&W2>j3i
zH+B{Qk9vzA|E+}cq!eiDD{JRnzkdBD&^>Uod+-*}Gjtp1<(HS2Gr7Z+ePiDNKTX`}
z7gPcLLe_w=dT^=+;EQU8XYLNqvVjpXd-U18vFEkG`19HcNgXgbUnh9+01&>cudi=t
zXlQC`YH4ZVa5(Ml?Ok16Jv}{reSJ@#KIQZIBO@b|laoTBP%IYD&CSiv&o3-2EG{lC
zFE6jGtgNoCN~O}ZwKch1zOk{fxw*N$y}h%uqfjW6N@ePj$u|hZZjzU$J1MPvb!IV{
znsSi0W~8D55dxEVqsE_G8QZiZ>|>Gl1VHzX<WUHOkOX%^wku_+o}GdW%DQ58n!Rsy
zyu5qhc8M&D$!D!IkH==Le>pV&aw;~%`63_ZOnWu&m!jpXk&fu|L3v7ybar3E=5gIk
zHH{%HM)sNid&nVyf77B|nZ(zC9xi4TOU1OsPx;!=!}tM5Dowz_5xFBZ#IiP3<cu)6
z`WS4OzOcKXw_ce#<ADt860IXC2Y4%T<=~O+s26JwVns7sZzE-yNO*+DilvI>k*vK$
zmd*5|*4EYrX+D<ncP?~pZ?K%H{SJKxk`51N5Z1hOvpCT}LAL+tNC~%b{hWGk`m@UY
z*#%erU9YM(Y}j!eZifOrthRw;Gov#UPGD&Tcl#<QqQAF~hAzpg1<c=S48LKSMMIyS
zc%#0aNatWFL7Rg9#BVq5VfBM_c|(G;6*SZq8gc-c%YJRo1=4V7(`ZrKKtHhpl3aWY
zlEV(0=@416@{7G2AIe2X7*PU)6KO&hsGwKXLfkDKovJV~gSKO(w`d}JPDrg@b%V9w
zuQSvI8EVbxM<-m<_`%j+`zlNdpR6@&U<L;V53RK2+H_pvEciD!VimFncl_;izD>l<
zy_z+V#ErgVRZ1{}RV#&UOU%R@A`wPp|I4U1YKyO!jjY@nOyb4)V4#na=J$?uo5RL$
zn<+395@pC3ww+`Y`Ir2;Cx(ir^hpNG`y3?tVu`7qxm|;;b=c1%FLW+*klO($^3geA
z2NYvx5IpyfVS7WRtUcTuK3WQW5WjkDE^1j<SMj>Umccr64!V?~!>fdMny~pGUs@?!
z6n9AX+n~v}@}r*TAl=?fR9r2KM{71*Ed!^(Ky}K^$Y79&hO9E7>DnPo@$Ib~yf2!<
znDd%7KkxNljm{#YljSm|7Lk=2e(cS8G3dYe#r~nYZw_e_Ij%CzS6!v`(-$Er-55?l
z+j8QQ#8_cU@XD|0!Q8;lUaWdlKD(MMlT~ODTdr{%FKsJk4J2%*BJ3fzPGt_Zw$K!&
zChs_dS4|<37SRzZD8(LSux?@dyiujxz_X|*GuT_gHisK^h-MIJFYi2qRfMf&MAdNv
zy-*We`;R1SQ#e7QhlWTx|7-e^$l>wJ<HZep&9nj+3A=d_N$iO3i5k}?GS3q6AI3$F
zUFNY(U>Av=^V?mS6Ii@UXF@ynblhuf1{jx_tLvE-u(rM%Oit{aijFSm)8fgT=|9_h
zw}(4o%I`L`tjUoxM>Q4VJ4CplUM^509^c2KpRm+~n{;{1yCU;{Ev)&!8S4?()hxkH
z>l8-kF6ZKX_CVuP%`$haYZ#WZ@nSgE@-Un*YkuaBUc+%#P~G6nH0=~>;<OI$l~2u~
z<#w?1Twc_FO4$N&M^apEU*SL)%{O?hoX5w@A_UY%mYk|hy#MpmH2oB+kb=+1lxjc@
vOFxcnCFZdL+h1-b=Dh>c;dhRxDy2&Jm_<%2-)so{xFNg<exCKGBCh-ssj+Hu

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 5fd242e36988d73859580d2b578798456e1e6daf..878c24089a59702c5b9fd48d84bd96c9126a63df 100644
GIT binary patch
literal 2710
zcmdVc`BT%^769-lrB>Ms1(XC3m3^xb2)hV0>`MidRd_5<jRIdmcBG2RHUzCAq7YhB
z1O!1KQnnBzffR|vu!}$-Kw{WZOi0-2^$&PIyqP!CzRwSL?m2UQx^vIDH^<8ZEp_O~
zAs7rM<?Q6}BMi154ukEx_l+3H4757Og2Zz#Hy=k3?%ThAznGZVSK{JdfAI})Na7$M
zAt@m(Eh#A}1<1<D$jHdb%F2DG^sSPz!eJF9gqpId`e8ur=#itxQ~-_Ra5x-sTub$Y
zwwjiXy1KdsplfhU-{`o3@d=}onnp-XW2BZbQd?VF2RLP>2bh@anOf)rW|oGAhDLye
zjj@%jvDNAC0c*RHHfNAX<SF2^<0(5w6B83tz#eU8W`=TfLH*!r;pA><X=w$xdRhZ+
z-nM|J&uPHR_q3Pa8Q|=Bd!GOY2M0&LK&OCEXCN@l&CSg{G|KZ|m%M<8%ifU~A0HoI
zUtd1}bM1U|yuZJHKtMoXU|<jsml_-#9CAG^Bq9Am;*HS6jL@W?BGT_fMn*<OMg99`
z&PCu>?q%S1J_dt{&iOeuHuf6!aeRDyB2ZYCl$4a5oSgFbSq84^=C9SafM+$CnVGlC
zU)=$o*Wayd%*x8j2C4`-IXU^S+OhS-d-v}B+|>2pck;uQ?n0oo=h34_MMXu$0I9E-
zM0)~szIzIE(Mw87N-6JgINUG5AH(>*vEOJPp3^5P-cMBm3})rPbk*R@3t(vG#W1V7
zy1E7!nX4I{e+i7SYiny88X6iK8wmtLb8~Y`OG{f@8<9xt=;$DkNS&RXU0q!i3Z=KV
zx38~{Mx)W`bOwVlI5;>oG&DRsJTfveHa0dfF)=wg$z(F8r>AFTW>_rN?Ck8^+}!;9
zJcq;Ka=A-OOUuj4D=RBJ9&dGZmCxr31cJ4-HK9-_5{Wi8Ha0gmx3{-<c6N4mclY-8
zuuQ|3FxY`=X9qi<q>|;yjiTY}2rA^JZ{nKwmOvm@dIerVy9DUuY2>=;o%m=F=!Spy
z@+9U;ea#gnRS^+%t3kn8UmNK}5ZCV5b4Jo)7>gCWt&%PCGJewbJ|4dnNsr@|ws2_r
z%IfEhx%&vNa0iz9w+HT{vMF}Qr8OYgoJ^;`Jterj1067GOP@Fh#V@eQG2>9r0%S&E
zRJ~rjJ2PHB8=Z|mo49f$p{_M)BL6L_L)cySK0BZMDtW^{wI|(PZ}xn8_o@8m`ISbc
z3uZ!<fWy>rl7edZ!)2`?)aOg#vgo>gtBj9LS1o@~l|vV;m|uKT6Ne6w`-h!^?04Pu
zP|8SN-D6xwHCxp{J9qX2hnD(A%0zV0&Ks^5#U{GL5mkA!RT4^uX;@Usk4jWA+wV=T
zmxHY$byy;U9a)ZygwnY0Iff~W(Qd|r29%-sLikyujCN46IrvsaI_Uw*0u+}k(P%;G
z(@(n@_dyLx@QhcQ(q2@E8zR=U^Rw+eT3z7QI=Qoy2OLCP_&e(WF9oV?LchgMQ>mqB
zWFnlfMn$wQ2_dbt2xiq&8PX-{;cDunEV^Q(R^=|H2-|iP>oM7a86z&RAhVRbaIOnG
zEkW7T$QDCyHj0XYY90%I@|#E(vKD)$WYJ|!WwA4VROH*ii5C3rs~?+|m6ILd!L6KM
z#2fn&$&P=|{anz-lA=prUs)Wn)NFmGh3JMTy?j+cR!;vXCp4sATr7HGAYaP3-@$5L
z;AUB|uR%UsJuI3u8(0^pfz=J}hCX<Y(zfT~Sd|05a5W3=uuSsqxo+?BlUNg@U~^~J
zsHq#BsiZ&0skwNUNVt4c1bebE#_~p5-ML)6(>W+D!W3Jkx~>Z;aCNb2Q#>*=gDg+1
z@c~hB9=3&!Y(Hu+=nY5Xki1@&_JB9s%#EHhAP~?KJyV>GEONuu)IKQvhfZ&OEh1dV
zZ&$~L?0hni*fsrp8)fl&F%yGDq}s#RZq$c;ZjvOMO`(K0v++~%Hpt{r8S<8m^_MV2
zLM6&NhCC+0svPaQ8#WflYwN+uqKS&8lH`{K%IRm|YXM`%l1!_sf`iZyCd~f-XZ0CR
zU3~6OA181{@}=I6@WPd(^(wyN@{><k4OXR~;v9{Z$|h;H;<Hh@?|N2i@5HHUVZU~_
z!ty-a-P5<jJmt}unyS>2qTq$daz_IS)a%;Lxj3Msr^US!2W@}$F3QW?SxRNE53Sw^
z2+P=FCG8xbyxC>5nxhzntk8@&C`bq+eKotc&OgSq;5m_OI2qfV(YU?EIUN<#?SuhW
zmux()U@7N+GP<u)>La_uFuUd}w^0iwa#SIHbPrlB`qIWkP1gDxI%}q#-}5C>WUY%B
zze|x*ZERPvQ40u5hV4Vkn8{3$G+Ae~AXT09X|QLW{HJIuS}oB5p1#@tB5YmAJywv7
z_awFKv6<F_NB7YbMg@^)yF^i;s{Z2!?|<<I?upy_;lhNWRR!RK33GPzaHu^Kdh0J+
CNyX;?

literal 3435
zcmeI#eKgcr9{}))?J1JCZPhRurZOuuwjmQDFOygqEOs>!6>F21kr<|;#LUG0@)ix2
zYRc*b;SrOUQ6^)EiM&iTk(r4dG{eeH#MoQs`Qv&1c+PqDoc-_VbAI=nd++ai?)m-h
z?|bh(Kf1S<+j@0<br=k`-hIETFAS!FfWcN}uT=#-{SVw@K?l>@(+>}tt5j4}R8>{K
zSiSlmAFTz{*Qo*PG}dWqYG`Pz2efsxw6wIfwRM26HtGT!H*J6$=;`TgG(^Gyq_Muf
zz5#&Ria;O?x1y0~QzIiI6biKkFvo1Qu-pb<cA8+YXiKaqU}a;r%hnvQv9qwS*s)^=
z#@4~oe(yKH9w#goYqb||<%GAkw%!G}xY^j)-~habt*xyc;NfNeEn$zRkAs7QBS7%m
z3wZlGIXO8yJG;2JxVpOHfdHaAKn(Tt^gIv}PB`+DH*oB@PgtaHc$A-?pTEC<KtMoX
zVBo=n2Z==DA>bq>C@3g6;mqO0vmuEoA>`C!XVSyM!otJDe>_Kzh=@22T=+RMGBTQ;
z8*?!)Ha0d6x)L8Bf9lk!goK1dAip&6av7OSPD)BjzH*&Hp`0zPNGZLQdiD0XYj@5A
z*YBpKrCqprFC8ea$*8EKQmHiH)<5ZY?q95I{292{4Arz`XJ_XE_aEgowCA%PUj`m@
z6aY=!!oorZ!0u+SpA-RYJ;lHyeo0BmFPx{PrKM#Z&#nTUgV(x-uLE5IX1CzRljr3C
zUs(S1)vr%SDuBMxivHKPo{ilG2F7j=itYkKlDoriDgnWGRaI4Wb#-lRZCzbmeSLjn
zV<U^jYHDg~X=!O~ZDq6BZEbBF4yU7|gU91_cX#vo{Jy@vfq{X+!NH-SA%Q?36beU2
zN5x{XL?W4(n2<`PQ&UsZ)6;L?zLm@6v$L~vb93|a^9qGxVPRo$adByBX?b~BsZ_44
ztSm%NhQeU#Y3{C0e&mw3uNE36(h=O*?~5v2hs?u9eX*v*ZGpLAot6dHa;;JHPTd!N
zYx9EqI`wPs!0B6$>}SHam-CjFOl2+DQOfw0xdrLmWb??xnbJ!q7yo$qp;@MI;43Kd
zJ&GrTuq^Ln*rf0OZ;|OwX$hBSicLnckFM=vk>m!ukWI%$I=c(5mWT<+j5}JtkX@l|
zUr!WRv>S3uu(LD`m+;m_7KVADTWP0Z0NIC5aR?O%{}T<9-#WUeu}hoYa+a$ZOKOAf
zObQSyTH<d!You4}%3DupaQX&FzeWigNpk~cJIxu!(Dvxj19M)C<b4^YSWaJ7Rs)R*
zhsWr+VRw$8pzveOctlSpITKfuGpk3k+9I|PMeOS!eh$ROAy^5Izta=OC{xUoG8|1;
zf{WwX4fixp5}>rNouDn8zC45*jfvh3X}b~P5P?}@_wE7<%63vbiktHow|OR~J`!UB
zc}Z}!+FX9&^7)3#;h*XgiqkI~_)7gxf$6y3R|?h0vXw7HzqvwN>f`}u?{(YInL4{6
za}MbtWA1R`^kR@G0^D0iDq&4LAEmsB8ws$@5qFASb{WW<xS@r*Zs<6~82ZK@9_a#Z
zGBD+}j5=yHn}KlIK^d9~*EE83qlF(bdbm|ZAJc55Il3>i>Pm`0grnVp9M5d3a)|$!
zizm3%YD1*%f-&f5FN5rwVT@fZYCQee<L)8WWN)Y-R-#5kI~2#A_PB4R&BZw81$%R%
z(6W>s$(EwlqiUr5&l&h%mlF>s!$~=-F=xk@+Ur^HmQJ!6oLjjjg*4tG@9p^w-$Crd
zK|d^JN|9*IFaLdUUcMymPg9VEc+MC~TzMLCDXD$<Z~~0f2u9e<P5%&FFGH81G&jOy
z9*c1c_X_Rb)2g+pnOO}1$oie*73sKOb~n-SLqGRRYG%Kxr{3Y+Bd6OQoN{b^Nu{;B
zN>`a=lA2>2pfcHFsL0YMIhA(=;rL*<sdeQd`uF>y>+fKBQKMa@%QF;v24;U${^pQJ
zg#B_A4=qb$s3{c;7#*afGxF%4h9WwWUz{H_n?P0(E=irGtAdw`uIBZtHq+YOL4z}P
z;~fkmiuFxS-AKZj?rF=!mE>=JjYoKSXw9HB(KpwSb-1}KYj$z6a|S$JoBQN)^&q=^
zBs<j2m{aqrAo1>5&c{q+=Bkqpk%ENtC);CrchD(Yi<HOwe2pL$w-l-1*-^)$CJrdQ
zt(Kox+;B!<_G1L&(%}OR*Q93KjUh&5BKy?u>kpLqsF9v5y~%kN6R}A5pdB5rwf<N2
ze|}WzUwgB^CH#9UXl~d%`SntYT&;Hod@azyWVc9I58)1A61zHT-YHUt3=K=hnEyG|
zAXSPBEO3Q5^^4ru%KFIR(%E}RT{ov$oSwa0Wh7wxZEY@#KNbn)R@om5>pi3Q^8Fwa
zgVJ1LM^z(`#NI?R0q;I8SeYPd^U@PH9xuzJtJ;D6?$L)i7t86avg{)pNFf70Kbj})
zOU_L1SJe+>zo*9bQU;dV6Z?tg`J10=vQ20{oO6Hkg%`bl*+;2V@;L@^8V@y(b83EK
z&)djX(&=uJAI=*N(8NqRGUGeKr_)v7M90a5^6K`P0s^5K#oaI+A~SxNf=+Dmw{eV!
z-W2@4n2x-N;IFy8u$<FABd0_ck@1je#rW?>GsX<68Oitza6)S-MrOEFWzytVaBz6D
u^8T=uG~`uBENaK!d<Pr&T>knT%sb{9VJ%7oLFwSH3FeOXa;<U>IsYdKtgA!-

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 6934353e57e90ce9e22c38f9731b9723a2cfe0dd..f4eaa065b590073e860100f4dd63543e9ef41702 100644
GIT binary patch
literal 1753
zcmeAS@N?(olHy`uVBq!ia0y~yV3J{AV4T3g3>3Mv%d-GTJq+*(aRt)M%*;GIJpBCp
zLPA2~;^Gn#5|WaV($doM^70A_3d+jLYHDiw`uc{3hDJt4#>U3x=H`}`mR43)*4EZG
zHa2#4cJ}u64h{}ZPEIZ^E<Qd!!NI{XF)^{Rv8k!4X=!PBd3l9}g~i3i<>loyH8r)h
zwG9mo9UUE=ot-mh&Rn!;(UK)gR;^mKe*OAw+qUi8xpUX9UAuSh-nVbx;lqcI96560
z#EDa<PMtY(=F+80SFT*SdiCn{>(_7JzJ2%Z-G>h!K7Rc8*|TTQpFe;7`t|3}pTB(h
z^7ZT2@87@w{rmUdzkmP#|7R$>UCF?}y4lmkF{EP7+dIe4#hNm>U7UZ<`vnWf!ZyBz
zY(h~D43+=cl{QIK^}p*}m%7%}!uj;2o0HP-AC2V@f4-05wGg|fj7s5zBaVZCk@LE@
z`@X-8qs;DK&rTlSZ~c*@Fz40$=ld$YUKTztaD18F?mzFRW~<NJ7$$Sw?xDc;e|4{(
z-Q{05=ZE#RuE#UaTOL_2Z~x(hGXK7kNADxF`>vm>ZH)c%@x|HO+wJS$90@+MacTLz
zz2A417Czqs<Sd>qzpM8B@9RhXm&+>iO|tNKq|n){LOEmG*4s@RE&4X!1(JN5?>Bwy
z-e1sREv+YEUpUpdX7|IUjp<J{#CkNvdOX48&ihmf{hZStx<@^9Q}<7dDwIjvKk=6C
zql$;0e#V*y?Ot~MzvXw{cTy{3uW}Vitc<+^A(=qzt4xJ5E;8-H$Nwt!E$w(*@Mwqq
zk&RQ7AOHBU_q+d>FOAzRr3=sO`T4Y0IM(WeS-NuH%<Xm7Us=wd3OZ6~QFx{!S>Sk&
z1sm-dZK01MvX_L(99AmSF$>b}OYF4>lU^x$e1n_J>fS5!<c?1cH~;YA_VaxQudcqY
zZyr=#B{SXcZb8Js&GvJCvzh1p*?GrfZF*|N!^p^dkTG0^Ys^8$G+KzsfQ)gFVHZ69
z@Q9&upQDWNBZ)!62<trD^sz|{M0Q>40FsmRV*meolb63EVUH^?8(8g^H;*y6r_`q!
zVX!R1KrIqPKC2U^PQKo#tGrbNjF$X$%bLIcjN-mq1xuza&antO?N}zW@~MJ#-<6^s
zUH7cWF6v~UzTCHFL8lA1Nw0ir@Voa)(TuBZS@CsG@7!MV=l!oD<*jRycTS9&w(*{a
s?&*m9CDTH6fG$a+QU;<|G5FGc^^`q3I~G=!0_!LSPgg&ebxsLQ0Q%k882|tP

literal 1746
zcmeAS@N?(olHy`uVBq!ia0y~yV3J{AV4T3g3>3Mv%d-GTy$$dQaRt)M%*;GIJpBCp
z;^N{G5)zV<lG4)B3JMC!%F23rdPYV@#>U1bCMMR_);2aac6N65_Vx}A4vvnFE-o%U
zK0d+0!J(m{;o;$tk&)5S(J?VGv9Ynq$;oMHY3b?d85tRQd3pKy`Gtjr#l^+t<>fUs
zHMO<1_4V})4GkR~9i5$>GiJ<~IdkTsMT?d!S+a8F%2lgYtzW->>(;H?wr$(BYuE1G
zyZ7wbvv1$NBS(%LKYsl5>C<P<oVjx4%GIk^uV24@>(;H?w{PFQd-w6<$IqTUd;a|S
zix)3mzkdDY%a^ZTzkd7n?fdudfB*jd_wV2T|Nq~JAJAZ6U|rzp;uumf=k1-7n?hVA
z+%B$G>Z)zFP3o>~=ZzB;balx2_q|?*^LTmxD}kx=BC-Px_w-m;Yo*^m>0n{`jWuGr
zg~ua>&Sn+9NrQlqygbh8=idj$M>hH|@3;SU_+WcS^7MaopI$%TZ}CH<@Xe*^;{SJk
z`FL=-j_C2T{dVch=KpsUB-`yM`S3kLt1mxp=P9<l+FuuT7W3N|gM}_1{?EDd{kz5H
zdH45K{d-V+WTW%@J>~zOPoG@fK2N#t@6WFjZ-1}<Z}Iczh2|rULhPP0Duoj$XB_u?
zn|ClmX7<hdO&cw?Z92^Q`2GFAy}W;R9%p^Le%`J#Y;|`YH*HK$RTk^f6zlN>la(JR
zw-@aGH&Z4?bxn*q#pj-NbmLUnzANt(`*w@#$=zK!@s{b`%C9%fC6u?Wj#A`P-r5Z%
z6@cv3Q3`!$JCc(hRX7~kC{~!`Bg5ZeacxtojQqa(rv~fy?tGZr=OU9{{qy$g_MdM~
zwQaW)DxCASH=14UL1bjNg_&C4=Fa3JfkzA<X*`lB6e;Yn=(2E=ag|Z-Q|c3R7d+mv
zxPt=eHNwZUl(#;bk@_eiZ%LTUW-po7y;r)D!#b1qPQ2Cpc*n0VPyg?|eqR1J+jRZ^
zTON44Jy;l1{rUiJJ8RANM;r4C{{Gs_>Yin*z4_SYO^-a*TBP+_gvqQFJ+32od=ki9
z)kimaXzd3AA+Scco%J!Rt`LwET`LGARqxh4ymj&J&Bsk2<sR+${!QJzJh`9ySanA-
zCk@jLFzH;9bI+Q;;{==EcZ;CYZr^}}S(zo2Q2PdCMNuoMUU}!1b@R+WAOT9QH&0b5
zZ#{2U{-!kS-{waix~n4!mP~V91GHZW7+I;j-hEd#84sS)il{>Ki++gf3Jssr7Yu-v
O6N9I#pUXO@geCyGyzOED

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>