use_calibrations_each

<code>use_calibrations_each</code> wraps <code>use_calibrations</code> to take each set of
given calibrations and use it independently as constraints for BLADJ or PATHd8
to date a given tree topology.

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_each 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>...</dt>
<dd>Arguments passed on to <code>use_calibrations</code><dl>
 <dt><code>dating_method</code></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></dl></dd> <dt><code>type</code></dt>
<dd>The type of age to use as calibration. Options are "median", "mean", "min", or "max".</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 by using a given list of calibrations independently,
to generate multiple hypothesis of time of divergence — use_calibrations_each

<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>...</dt>
<dd>Arguments passed on to <code>use_calibrations</code><dl>
 <dt><code>dating_method</code></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><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 by using a given list of calibrations independently,
to generate multiple hypothesis of time of divergence

use_calibrations_each: Date a given tree topology by using a given list of calibrations independently, to generate multiple hypothesis of time of divergence

Description

Usage

Value

Arguments

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