datelife_use_datelifequery

<code>datelife_use</code> gets secondary calibrations available for any
pair of given taxon names, mined from the opentree_chronograms object,
congruifies them, and uses them to date a given tree topology with the
algorithm defined in <code>dating_method</code>. If no tree topology is provided,
it will attempt to get one for the given taxon names from Open Tree of Life
synthetic tree, using <code>make_bold_otol_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

datelife_use_datelifequery function

<dl><dt>datelife_query</dt>
<dd>A <code>datelifeQuery</code> object, usually an output of <code>make_datelife_query()</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>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></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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Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object. — datelife_use_datelifequery

<dl>

<dt>datelife_query</dt>
<dd>A <code>datelifeQuery</code> object, usually an output of <code>make_datelife_query()</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>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>

</dl>

Generate one or multiple chronograms for a set of taxon names given as a <code>datelifeQuery</code> object.

datelife_use_datelifequery: Generate one or multiple chronograms for a set of taxon names given as a `datelifeQuery` object.

Description

Usage

Value

Arguments

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