use_calibrations

<code>use_calibrations</code> combines all given calibrations and uses them as
constraints to perform a dating analysis on a given tree topology, using BLADJ
if it has no branch lengths, or PATHd8 if the given tree topology has initial
branch lengths.

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 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>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>type</dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd>
<dt>...</dt>
<dd>Arguments passed on to <code>use_calibrations_pathd8</code><dl>
 <dt><code>expand</code></dt>
<dd>How much to expand by each step to get consistent calibrations. Should be between 0 and 1.</dd></dl></dd> <dt><code>giveup</code></dt>
<dd>How many expansions to try before giving up</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 combined set of given calibrations — use_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>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>type</dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</dd>


<dt>...</dt>
<dd>Arguments passed on to <code>use_calibrations_pathd8</code><dl>
 <dt><code>expand</code></dt>
<dd>How much to expand by each step to get consistent calibrations. Should be between 0 and 1.</dd>

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

 
</dl></dd>

</dl>

Date a given tree topology using a combined set of given calibrations

use_calibrations: Date a given tree topology using a combined set of given calibrations

Description

Usage

Value

Arguments

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Details