get_best_grove

Get grove from a <code>datelifeResult</code> object that can be converted to phylo
from a median summary matrix

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

get_best_grove function

<dl><dt>datelife_result</dt>
<dd>A <code>datelifeResult</code> object. Only needed for <code>criterion = "taxa"</code>.</dd>
<dt>criterion</dt>
<dd>Defaults to <code>criterion = "taxa"</code>. Used for chronogram summarizing, i.e., obtaining a single
summary chronogram from a group of input chronograms.
For summarizing approaches that return a single summary tree from a group of
phylogenetic trees, it is necessary that the latter form a grove, roughly,
a sufficiently overlapping set of taxa between trees, see Ané et al. (2009) tools:::Rd_expr_doi("10.1007/s00026-009-0017-x").
In rare cases, a group of trees can have multiple groves. This argument indicates
whether to get the grove with the most trees (<code>criterion = "trees"</code>) or the
most taxa (<code>criterion = "taxa"</code>).</dd>
<dt>n</dt>
<dd>The degree of taxon name overlap among input chronograms. Defaults
to <code>n = 2</code>, i.e., at least two overlapping taxon names.</dd></dl>

Arguments

Get grove from a datelifeResult object that can be converted to phylo
from a median summary matrix — get_best_grove

<dl>

<dt>datelife_result</dt>
<dd>A <code>datelifeResult</code> object. Only needed for <code>criterion = "taxa"</code>.</dd>


<dt>criterion</dt>
<dd>Defaults to <code>criterion = "taxa"</code>. Used for chronogram summarizing, i.e., obtaining a single
summary chronogram from a group of input chronograms.
For summarizing approaches that return a single summary tree from a group of
phylogenetic trees, it is necessary that the latter form a grove, roughly,
a sufficiently overlapping set of taxa between trees, see Ané et al. (2009) tools:::Rd_expr_doi("10.1007/s00026-009-0017-x").
In rare cases, a group of trees can have multiple groves. This argument indicates
whether to get the grove with the most trees (<code>criterion = "trees"</code>) or the
most taxa (<code>criterion = "taxa"</code>).</dd>


<dt>n</dt>
<dd>The degree of taxon name overlap among input chronograms. Defaults
to <code>n = 2</code>, i.e., at least two overlapping taxon names.</dd>

</dl>

Get grove from a <code>datelifeResult</code> object that can be converted to phylo
from a median summary matrix

get_best_grove: Get grove from a `datelifeResult` object that can be converted to phylo from a median summary matrix

Description

Usage

Value

Arguments