get_calibrations_vector

The function searches DateLife's local
database of phylogenetic trees with branch lengths proportional to time
(chronograms) with <code>datelife_search()</code>, and extracts available node ages
for each pair of given taxon names with <code>extract_calibrations_phylo()</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

get_calibrations_vector function

<dl><dt>input</dt>
<dd>A character vector of taxon names.</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

Search and extract secondary calibrations for a given character
vector of taxon names — get_calibrations_vector

<dl>

<dt>input</dt>
<dd>A character vector of taxon names.</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>

Search and extract secondary calibrations for a given character
vector of taxon names

get_calibrations_vector: Search and extract secondary calibrations for a given character vector of taxon names

Description

Usage

Value

Arguments

Details