diff --git a/README.Rmd b/README.Rmd
index 231ba6e..1e0777a 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -40,8 +40,6 @@ knitr::opts_chunk$set(
 ```
 
 [![Travis build status](https://travis-ci.org/venelin/SPLITT.svg?branch=master)](https://travis-ci.org/venelin/SPLITT)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/SPLITT?color=blue)](http://cran.rstudio.com/package=SPLITT)
-[![Downloads](http://cranlogs.r-pkg.org/badges/SPLITT?color=blue)](http://cran.rstudio.com/package=SPLITT)
 [![DOI](https://zenodo.org/badge/159803456.svg)](https://zenodo.org/badge/latestdoi/159803456)
 
 # SPLITT: Serial and Parallel LIneage Traversal of Trees
diff --git a/README.md b/README.md
index c782187..aa1d69b 100644
--- a/README.md
+++ b/README.md
@@ -29,8 +29,6 @@
 
 [![Travis build
 status](https://travis-ci.org/venelin/SPLITT.svg?branch=master)](https://travis-ci.org/venelin/SPLITT)
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/SPLITT?color=blue)](http://cran.rstudio.com/package=SPLITT)
-[![Downloads](http://cranlogs.r-pkg.org/badges/SPLITT?color=blue)](http://cran.rstudio.com/package=SPLITT)
 [![DOI](https://zenodo.org/badge/159803456.svg)](https://zenodo.org/badge/latestdoi/159803456)
 
 # SPLITT: Serial and Parallel LIneage Traversal of Trees
@@ -109,7 +107,7 @@ Phylogenetic Comparative Models: the SPLITT C++ Library. bioRxiv,
 
 The SPLITT R-package uses the following 3rd party R-packages:
 
-  - For calling C++ from R: Rcpp v1.0.1 (Eddelbuettel et al. 2018);
+  - For calling C++ from R: Rcpp v1.0.2 (Eddelbuettel et al. 2018);
   - For tree processing in R: ape v5.3 (Paradis et al. 2018);
   - For cloning and manipulating git repositories: git2r v0.26.1 (Csardi
     et al. 2018);
diff --git a/docs/index.html b/docs/index.html
index 24680f5..ba73389 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -169,7 +169,7 @@ <h1 class="hasAnchor">
 <a href="#used-r-packages" class="anchor"></a>Used R-packages</h1>
 <p>The SPLITT R-package uses the following 3rd party R-packages:</p>
 <ul>
-<li>For calling C++ from R: Rcpp v1.0.1 <span class="citation">(Eddelbuettel et al. 2018)</span>;</li>
+<li>For calling C++ from R: Rcpp v1.0.2 <span class="citation">(Eddelbuettel et al. 2018)</span>;</li>
 <li>For tree processing in R: ape v5.3 <span class="citation">(Paradis et al. 2018)</span>;</li>
 <li>For cloning and manipulating git repositories: git2r v0.26.1 <span class="citation">(Csardi et al. 2018)</span>;</li>
 <li>For documentation and web-site generation: roxygen2 v6.1.1 <span class="citation">(Wickham, Danenberg, and Eugster 2018)</span>, pkgdown v1.3.0 <span class="citation">(Wickham and Hesselberth 2018)</span>;</li>
@@ -180,14 +180,29 @@ <h1 class="hasAnchor">
 <a href="#licence-and-copyright" class="anchor"></a>Licence and copyright</h1>
 <p>Copyright 2017-2019 Venelin Mitov</p>
 <p>Source code to SPLITT is made available under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at the user’s option) any later version. SPLITT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.</p>
-<div class="references">
-<h1>References</h1>
-<p>Csardi, Gabor, Gregory Jefferis, Jennifer Bryan, Jeroen Ooms, Jim Hester, Karthik Ram, and Stefan Widgren. 2018. <em>Git2r: Provides Access to Git Repositories</em>. <a href="https://CRAN.R-project.org/package=git2r" class="uri">https://CRAN.R-project.org/package=git2r</a>.</p>
-<p>Eddelbuettel, Dirk, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates, and John Chambers. 2018. <em>Rcpp: Seamless R and C++ Integration</em>. <a href="https://CRAN.R-project.org/package=Rcpp" class="uri">https://CRAN.R-project.org/package=Rcpp</a>.</p>
+</div>
+<div id="references" class="section level1 unnumbered">
+<h1 class="hasAnchor">
+<a href="#references" class="anchor"></a>References</h1>
+<div id="refs" class="references">
+<div id="ref-R-git2r">
+<p>Csardi, Gabor, Gregory Jefferis, Jennifer Bryan, Jeroen Ooms, Jim Hester, Karthik Ram, and Stefan Widgren. 2018. <em>Git2r: Provides Access to Git Repositories</em>. <a href="https://CRAN.R-project.org/package=git2r">https://CRAN.R-project.org/package=git2r</a>.</p>
+</div>
+<div id="ref-R-Rcpp">
+<p>Eddelbuettel, Dirk, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates, and John Chambers. 2018. <em>Rcpp: Seamless R and C++ Integration</em>. <a href="https://CRAN.R-project.org/package=Rcpp">https://CRAN.R-project.org/package=Rcpp</a>.</p>
+</div>
+<div id="ref-Mitov:2017eg">
 <p>Mitov, Venelin, and Tanja Stadler. 2018. “Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library.” <em>Methods in Ecology and Evolution</em>, December, 2041–210X.13136.</p>
-<p>Paradis, Emmanuel, Simon Blomberg, Ben Bolker, Joseph Brown, Julien Claude, Hoa Sien Cuong, Richard Desper, et al. 2018. <em>Ape: Analyses of Phylogenetics and Evolution</em>. <a href="https://CRAN.R-project.org/package=ape" class="uri">https://CRAN.R-project.org/package=ape</a>.</p>
-<p>Wickham, Hadley, and Jay Hesselberth. 2018. <em>Pkgdown: Make Static HTML Documentation for a Package</em>.</p>
-<p>Wickham, Hadley, Peter Danenberg, and Manuel Eugster. 2018. <em>Roxygen2: In-Line Documentation for R</em>. <a href="https://CRAN.R-project.org/package=roxygen2" class="uri">https://CRAN.R-project.org/package=roxygen2</a>.</p>
+</div>
+<div id="ref-R-ape">
+<p>Paradis, Emmanuel, Simon Blomberg, Ben Bolker, Joseph Brown, Julien Claude, Hoa Sien Cuong, Richard Desper, et al. 2018. <em>Ape: Analyses of Phylogenetics and Evolution</em>. <a href="https://CRAN.R-project.org/package=ape">https://CRAN.R-project.org/package=ape</a>.</p>
+</div>
+<div id="ref-R-roxygen2">
+<p>Wickham, Hadley, Peter Danenberg, and Manuel Eugster. 2018. <em>Roxygen2: In-Line Documentation for R</em>. <a href="https://CRAN.R-project.org/package=roxygen2">https://CRAN.R-project.org/package=roxygen2</a>.</p>
+</div>
+<div id="ref-R-pkgdown">
+<p>Wickham, Hadley, and Jay Hesselberth. 2018. <em>Pkgdown: Make Static Html Documentation for a Package</em>.</p>
+</div>
 </div>
 </div>
   </div>
@@ -225,8 +240,6 @@ <h2>Developers</h2>
 <h2>Dev status</h2>
 <ul class="list-unstyled">
 <li><a href="https://travis-ci.org/venelin/SPLITT"><img src="https://travis-ci.org/venelin/SPLITT.svg?branch=master" alt="Travis build status"></a></li>
-<li><a href="http://cran.rstudio.com/package=SPLITT"><img src="http://www.r-pkg.org/badges/version/SPLITT?color=blue" alt="CRAN_Status_Badge"></a></li>
-<li><a href="http://cran.rstudio.com/package=SPLITT"><img src="http://cranlogs.r-pkg.org/badges/SPLITT?color=blue" alt="Downloads"></a></li>
 <li><a href="https://zenodo.org/badge/latestdoi/159803456"><img src="https://zenodo.org/badge/159803456.svg" alt="DOI"></a></li>
 </ul>
 </div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index e5af56c..82b6c73 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 1.13.1
+pandoc: 2.3.1
 pkgdown: 1.3.0
 pkgdown_sha: ~
 articles:
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 5261f79..449d6bc 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -9,144 +9,6 @@
   <url>
     <loc>http://venelin.github.io/SPLITT/reference/PlotParallelTraversal.html</loc>
   </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-At.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-G_EMPTY_UVEC.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-G_NA_UINT.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-G_PI.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-IsNA.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Match.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-NotIsNA.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-LengthType.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-NodeType.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-OrderedTree.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-RangeIdPruneNode.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-RangeIdVisitNode.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-num_levels.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-num_parallel_ranges_prune.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-ranges_id_prune.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree-colon-colon-ranges_id_visit.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-OrderedTree.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Seq.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-SortIndices.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-ThreadExceptionHandler.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-TraversalAlgorithm.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-TraversalSpecification.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-TraversalTask.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-TraversalTaskLightweight.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-BranchLengths.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-FindChildren.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-FindIdOfNode.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-FindIdOfParent.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-FindNodeWithId.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-HasBranchLengths.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-LengthOfBranch.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-LengthType.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-NodeType.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-OrderNodes.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-OrderNodesPosType.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-SetBranchLengths.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-SetLengthOfBranch.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-Tree.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-num_nodes.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree-colon-colon-num_tips.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-Tree.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-bvec.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-uint.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-uvec.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT-colon-colon-vec.html</loc>
-  </url>
-  <url>
-    <loc>http://venelin.github.io/SPLITT/reference/SPLITT.html</loc>
-  </url>
   <url>
     <loc>http://venelin.github.io/SPLITT/reference/SPLITT__OrderedTreeStringNodes.html</loc>
   </url>
diff --git a/vignettes/REFERENCES-R.bib b/vignettes/REFERENCES-R.bib
index 77c6490..4c6b179 100644
--- a/vignettes/REFERENCES-R.bib
+++ b/vignettes/REFERENCES-R.bib
@@ -1,10 +1,3 @@
-@Manual{R-Rcpp,
-  title = {Rcpp: Seamless R and C++ Integration},
-  author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Douglas Bates and John Chambers},
-  year = {2019},
-  note = {R package version 1.0.1},
-  url = {https://CRAN.R-project.org/package=Rcpp},
-}
 @Manual{R-ape,
   title = {ape: Analyses of Phylogenetics and Evolution},
   author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Joseph Brown and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and RJ Ewing and Olivier Gascuel and Thomas Guillerme and Christoph Heibl and Anthony Ives and Bradley Jones and Franz Krah and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Eric Marcon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
@@ -26,6 +19,13 @@ @Manual{R-pkgdown
   note = {R package version 1.3.0},
   url = {https://CRAN.R-project.org/package=pkgdown},
 }
+@Manual{R-Rcpp,
+  title = {Rcpp: Seamless R and C++ Integration},
+  author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Douglas Bates and John Chambers},
+  year = {2019},
+  note = {R package version 1.0.2},
+  url = {https://CRAN.R-project.org/package=Rcpp},
+}
 @Manual{R-roxygen2,
   title = {roxygen2: In-Line Documentation for R},
   author = {Hadley Wickham and Peter Danenberg and Manuel Eugster},