datelife_result_median

Get a median summary chronogram from a <code>datelifeResult</code> object.

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_result_median function

<dl><dt>datelife_result</dt>
<dd>A <code>datelifeResult</code> object, usually an output of <code>get_datelife_result()</code>.</dd>
<dt>...</dt>
<dd>Arguments passed on to <code>summary_matrix_to_phylo</code><dl>
 <dt><code>summ_matrix</code></dt>
<dd>Any summary patristic distance matrix, such as the ones obtained with <code>datelife_result_sdm_matrix()</code> or <code>datelife_result_median_matrix()</code>.</dd></dl></dd> <dt><code>total_distance</code></dt>
<dd>Whether the input <code>summ_matrix</code> stores total age distance
(from tip to tip) or distance from node to tip. Default to <code>TRUE</code>,
divides the matrix in half, if <code>FALSE</code> it will take it as is.</dd> <dt><code>use</code></dt>
<dd>A character vector indicating what type of age to use for summary tree.
One of the following:<dl>
<dt>"mean"</dt>
<dd>It will use the <code><a href="/link/mean()?package=datelife&version=0.6.8" data-mini-rdoc="datelife::mean()">mean()</a></code> of the node ages in <code>summ_matrix</code>.</dd></dl></dd><dt>"median"</dt>
<dd>It uses the <code><a href="/link/stats%3A%3Amedian()?package=datelife&version=0.6.8" data-mini-rdoc="datelife::stats::median()">stats::median()</a></code> age of node ages in <code>summ_matrix</code>.</dd><dt>"min"</dt>
<dd>It will use the <code><a href="/link/min()?package=datelife&version=0.6.8" data-mini-rdoc="datelife::min()">min()</a></code> age from node ages in <code>summ_matrix</code>.</dd><dt>"max"</dt>
<dd>Choose this if you wanna be conservative; it will use the <code><a href="/link/max()?package=datelife&version=0.6.8" data-mini-rdoc="datelife::max()">max()</a></code>
age from node ages in <code>summ_matrix</code>.</dd><dt>"midpoint"</dt>
<dd>It will use the mean of minimum age and maximum age.</dd>
</dl> <dt><code>target_tree</code></dt>
<dd>A <code>phylo</code> object. Use this in case you want a specific
backbone for the output tree.</dd> <dt><code>datelife_query</code></dt>
<dd>A <code>datelifeQuery</code> object, usually an output of <code>make_datelife_query()</code>.</dd>

Arguments

Get a median summary chronogram from a datelifeResult object. — datelife_result_median

<dl>

<dt>datelife_result</dt>
<dd>A <code>datelifeResult</code> object, usually an output of <code>get_datelife_result()</code>.</dd>


<dt>...</dt>
<dd>Arguments passed on to <code>summary_matrix_to_phylo</code><dl>
 <dt><code>summ_matrix</code></dt>
<dd>Any summary patristic distance matrix, such as the ones obtained with <code>datelife_result_sdm_matrix()</code> or <code>datelife_result_median_matrix()</code>.</dd>

 <dt><code>total_distance</code></dt>
<dd>Whether the input <code>summ_matrix</code> stores total age distance
(from tip to tip) or distance from node to tip. Default to <code>TRUE</code>,
divides the matrix in half, if <code>FALSE</code> it will take it as is.</dd>

 <dt><code>use</code></dt>
<dd>A character vector indicating what type of age to use for summary tree.
One of the following:<dl>
<dt>"mean"</dt>
<dd>It will use the <code><a href='https://rdrr.io/r/base/mean.html'>mean()</a></code> of the node ages in <code>summ_matrix</code>.</dd>

<dt>"median"</dt>
<dd>It uses the <code><a href='https://rdrr.io/r/stats/median.html'>stats::median()</a></code> age of node ages in <code>summ_matrix</code>.</dd>

<dt>"min"</dt>
<dd>It will use the <code><a href='https://rdrr.io/r/base/Extremes.html'>min()</a></code> age from node ages in <code>summ_matrix</code>.</dd>

<dt>"max"</dt>
<dd>Choose this if you wanna be conservative; it will use the <code><a href='https://rdrr.io/r/base/Extremes.html'>max()</a></code>
age from node ages in <code>summ_matrix</code>.</dd>

<dt>"midpoint"</dt>
<dd>It will use the mean of minimum age and maximum age.</dd>


</dl></dd>

 <dt><code>target_tree</code></dt>
<dd>A <code>phylo</code> object. Use this in case you want a specific
backbone for the output tree.</dd>

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

 
</dl></dd>

</dl>

Get a median summary chronogram from a <code>datelifeResult</code> object.

datelife_result_median: Get a median summary chronogram from a `datelifeResult` object.

Description

Usage

Value

Arguments