congruify_and_check

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

congruify_and_check function

<dl><dt>reference</dt>
<dd>an ultrametric tree used to time-scale the <code>target</code></dd>
<dt>target</dt>
<dd>a phylogram that is sought to be ultrametricized based on the <code>reference</code> phylogeny</dd>
<dt>taxonomy</dt>
<dd>a linkage table between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny</dd>
<dt>tol</dt>
<dd>branching time in <code>reference</code> above which secondary constraints will be applied to <code>target</code></dd>
<dt>option</dt>
<dd>an integer (1 or 2; see details).</dd>
<dt>scale</dt>
<dd><code>NA</code>, <code>"PATHd8"</code> or <code>"treePL"</code> (if <code>PATHd8</code> or <code>"treePL"</code> are available in the R <code>PATH</code>)</dd>
<dt>attempt_fix</dt>
<dd>Default to <code>TRUE</code>. If congruification results in NA branch
lengths, it will attempt to fix them.</dd></dl>

Arguments

Congruify and Check. — congruify_and_check

<dl>

<dt>reference</dt>
<dd>an ultrametric tree used to time-scale the <code>target</code></dd>


<dt>target</dt>
<dd>a phylogram that is sought to be ultrametricized based on the <code>reference</code> phylogeny</dd>


<dt>taxonomy</dt>
<dd>a linkage table between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny</dd>


<dt>tol</dt>
<dd>branching time in <code>reference</code> above which secondary constraints will be applied to <code>target</code></dd>


<dt>option</dt>
<dd>an integer (1 or 2; see details).</dd>


<dt>scale</dt>
<dd><code>NA</code>, <code>"PATHd8"</code> or <code>"treePL"</code> (if <code>PATHd8</code> or <code>"treePL"</code> are available in the R <code>PATH</code>)</dd>


<dt>attempt_fix</dt>
<dd>Default to <code>TRUE</code>. If congruification results in NA branch
lengths, it will attempt to fix them.</dd>

</dl>

Congruify and Check.

congruify_and_check: Congruify and Check.

Description

Usage

Arguments