use_all_calibrations

<code>use_all_calibrations</code> generates one or multiple chronograms
(i.e., phylogenetic trees with branch lengths proportional to time) by dating
a tree topology given in <code>phy</code>, and secondary calibrations given in
<code>calibrations</code>, using the algorithm specified in the argument <code>dating_method</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_all_calibrations function

<dl><dt>phy</dt>
<dd>A <code>phylo</code> object to use as tree topology.</dd>
<dt>calibrations</dt>
<dd>A <code>calibrations</code> object, an output of <code>get_all_calibrations()</code>.</dd>
<dt>each</dt>
<dd>Boolean, default to <code>FALSE</code>: all calibrations are returned in
the same <code>data.frame</code>. If <code>TRUE</code>, calibrations from each chronogram are returned
in separate data frames.</dd>
<dt>dating_method</dt>
<dd>Tree dating algorithm to use. Options are "bladj" or "pathd8"
(Webb et al., 2008, tools:::Rd_expr_doi("10.1093/bioinformatics/btn358"); Britton et al., 2007,
tools:::Rd_expr_doi("10.1080/10635150701613783")).</dd>
<dt>...</dt>
<dd>Arguments passed on to <code>use_calibrations</code><dl>
 <dt><code>type</code></dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd></dl></dd> 
</dl>

Arguments

The output object stores the used <code>calibrations</code> and <code>dating_method</code> as
<code>attributes(output)$datelife_calibrations</code> and <code>attributes(output)$dating_method</code>.

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Date a given tree topology using a given set of congruified calibrations or ages — use_all_calibrations

<dl>

<dt>phy</dt>
<dd>A <code>phylo</code> object to use as tree topology.</dd>


<dt>calibrations</dt>
<dd>A <code>calibrations</code> object, an output of <code>get_all_calibrations()</code>.</dd>


<dt>each</dt>
<dd>Boolean, default to <code>FALSE</code>: all calibrations are returned in
the same <code>data.frame</code>. If <code>TRUE</code>, calibrations from each chronogram are returned
in separate data frames.</dd>


<dt>dating_method</dt>
<dd>Tree dating algorithm to use. Options are "bladj" or "pathd8"
(Webb et al., 2008, tools:::Rd_expr_doi("10.1093/bioinformatics/btn358"); Britton et al., 2007,
tools:::Rd_expr_doi("10.1080/10635150701613783")).</dd>


<dt>...</dt>
<dd>Arguments passed on to <code>use_calibrations</code><dl>
 <dt><code>type</code></dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd>

 
</dl></dd>

</dl>

Date a given tree topology using a given set of congruified calibrations or ages

use_all_calibrations: Date a given tree topology using a given set of congruified calibrations or ages

Description

Usage

Value

Arguments

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Details

References