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

run function

<dl><dt>input</dt>
<dd>A newick string or vector of taxa</dd>
<dt>format</dt>
<dd>The output format</dd>
<dt>partial</dt>
<dd>How to deal with trees that have a subset of taxa in the query</dd>
<dt>plot.width</dt>
<dd>Width in pixels for output plot</dd>
<dt>plot.height</dt>
<dd>Height in pixels for output plot</dd>
<dt>use_tnrs</dt>
<dd>Whether to use OpenTree's TNRS for the input</dd>
<dt>opentree_chronograms</dt>
<dd>The list of lists containing the input trees and other info</dd></dl>

Arguments

Core function to generate results — run

<dl>

<dt>input</dt>
<dd>A newick string or vector of taxa</dd>


<dt>format</dt>
<dd>The output format</dd>


<dt>partial</dt>
<dd>How to deal with trees that have a subset of taxa in the query</dd>


<dt>plot.width</dt>
<dd>Width in pixels for output plot</dd>


<dt>plot.height</dt>
<dd>Height in pixels for output plot</dd>


<dt>use_tnrs</dt>
<dd>Whether to use OpenTree's TNRS for the input</dd>


<dt>opentree_chronograms</dt>
<dd>The list of lists containing the input trees and other info</dd>

</dl>

Core function to generate results

run: Core function to generate results

Description

Usage

Value

Arguments