use_calibrations_bladj.matchedCalibrations

The function prepares the input for BLADJ and calls <code>make_bladj_tree()</code>

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_bladj.matchedCalibrations function

<dl><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>type</dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd>
<dt>root_age</dt>
<dd>Numeric specifying an age for the root, provided by the user.
Only used if there are no time calibrations for the root node in the chronograms database.
If <code>NULL</code> or not numeric, the maximum calibration age plus one unit of the sd
(calculated with <code><a href="/link/stats%3A%3Asd()?package=datelife&version=0.6.8" data-mini-rdoc="datelife::stats::sd()">stats::sd()</a></code>)
of all node ages available for the tree will be used as root calibration.
If there is only one calibration available for the whole tree, the root
node age will be proportional to 1.1 of the age of that calibration.</dd></dl>

Arguments

Use calibrations to date a topology with the BLADJ algorithm. — use_calibrations_bladj.matchedCalibrations

<dl>

<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>type</dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd>


<dt>root_age</dt>
<dd>Numeric specifying an age for the root, provided by the user.
Only used if there are no time calibrations for the root node in the chronograms database.
If <code>NULL</code> or not numeric, the maximum calibration age plus one unit of the sd
(calculated with <code><a href='https://rdrr.io/r/stats/sd.html'>stats::sd()</a></code>)
of all node ages available for the tree will be used as root calibration.
If there is only one calibration available for the whole tree, the root
node age will be proportional to 1.1 of the age of that calibration.</dd>

</dl>

Use calibrations to date a topology with the BLADJ algorithm.

use_calibrations_bladj.matchedCalibrations: Use calibrations to date a topology with the BLADJ algorithm.

Description

Usage

Value

Arguments

Details

References