use_calibrations_pathd8

<code>use_calibrations_pathd8</code> uses secondary calibrations to date a tree with initial branch lengths using PATHd8.

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

use_calibrations_pathd8 function

<dl><dt>phy</dt>
<dd>A <code>phylo</code> object with branch lengths.</dd>
<dt>calibrations</dt>
<dd>A <code>data.frame</code> of secondary calibrations for any pair of taxon
names in <code>phy</code>, usually obtained with <code>get_all_calibrations()</code>.</dd>
<dt>expand</dt>
<dd>How much to expand by each step to get consistent calibrations. Should be between 0 and 1.</dd>
<dt>giveup</dt>
<dd>How many expansions to try before giving up</dd></dl>

Arguments

Date a tree with secondary calibrations using PATHd8 — use_calibrations_pathd8

<dl>

<dt>phy</dt>
<dd>A <code>phylo</code> object with branch lengths.</dd>


<dt>calibrations</dt>
<dd>A <code>data.frame</code> of secondary calibrations for any pair of taxon
names in <code>phy</code>, usually obtained with <code>get_all_calibrations()</code>.</dd>


<dt>expand</dt>
<dd>How much to expand by each step to get consistent calibrations. Should be between 0 and 1.</dd>


<dt>giveup</dt>
<dd>How many expansions to try before giving up</dd>

</dl>

Date a tree with secondary calibrations using PATHd8

use_calibrations_pathd8: Date a tree with secondary calibrations using PATHd8

Description

Usage

Value

Arguments

Details

References