plant_bold_otol_tree

tree

plant

chronogram

otol

bold

Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths
proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence.
This package constitutes the main underlying code of the DateLife web service
at <https://www.datelife.org>. To obtain a single summary chronogram from a group of
relevant chronograms, we implement the Super Distance Matrix (SDM) method
described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>.
To find the grove of chronograms with a sufficiently overlapping set of taxa
for summarizing, we implement theorem 1.1. from Ané et al. (2009)
<doi:10.1007/s00026-009-0017-x>.
A given phylogenetic tree can be dated using time of lineage divergence data
as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>).
To obtain and apply secondary calibrations, the package implements the congruification method described
in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods
including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8
(Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck
and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith
and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).

Luna L. Sanchez Reyes

datelife

Scientific Data on Time of Lineage Divergence for Your Taxa

Brian O'Meara

Jonathan Eastman

Tracy Heath

April Wright

Klaus Schliep

Scott Chamberlain

Peter Midford

Luke Harmon

Joseph Brown

Matt Pennell

Mike Alfaro

Emily Jane McTavish

plant_bold_otol_tree function

A phylo object with 6 tips and 5 internal nodes<dl>
<dt>edge</dt>
<dd>Integer vector with edge (branch) numbers</dd><dt>tip.label</dt>
<dd>Character vector with species names of plants</dd><dt>Nnode</dt>
<dd>Integer vector with the number of nodes</dd><dt>node.label</dt>
<dd>Character vector with node names</dd><dt>edge.length</dt>
<dd>Numeric vector with edge (branch) lengths</dd>
</dl>

Format

Luna L. Sanchez-Reyes <a href="/link/lsanche7%40utk.edu?package=datelife&version=0.6.8" data-mini-rdoc="datelife::lsanche7@utk.edu">lsanche7@utk.edu</a>
Brian O'Meara <a href="/link/bomeara%40utk.edu?package=datelife&version=0.6.8" data-mini-rdoc="datelife::bomeara@utk.edu">bomeara@utk.edu</a>

Author

Some plants chronogram — plant_bold_otol_tree

A phylo object with 6 tips and 5 internal nodes<dl>
<dt>edge</dt>
<dd>Integer vector with edge (branch) numbers</dd>

<dt>tip.label</dt>
<dd>Character vector with species names of plants</dd>

<dt>Nnode</dt>
<dd>Integer vector with the number of nodes</dd>

<dt>node.label</dt>
<dd>Character vector with node names</dd>

<dt>edge.length</dt>
<dd>Numeric vector with edge (branch) lengths</dd>


</dl>

Luna L. Sanchez-Reyes <a href='mailto:lsanche7@utk.edu'>lsanche7@utk.edu</a>
Brian O'Meara <a href='mailto:bomeara@utk.edu'>bomeara@utk.edu</a>

Some plants chronogram

plant_bold_otol_tree: Some plants chronogram

Description

Usage

Arguments

Format

Author

Details