writeAncestors

This function writes a tree to file with ancestral character states and (optionally) 95% confidence intervals stored as node value.

phylogenetics

comparative method

input/output

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

writeAncestors function

<dl>	<dt>tree</dt>
<dd>a phylogenetic tree or set of trees as an object of class <code>"phylo"</code> or <code>"multiPhylo"</code>.</dd>	<dt>Anc</dt>
<dd>a vector of ancestral states, a list containing the ancestral states and 95% confidence intervals (as from <code>fastAnc</code> or <code>ace</code>, or a list of such results.</dd>	<dt>file</dt>
<dd>an optional string with the filename for output.</dd>	<dt>digits</dt>
<dd>an integer indicating the number of digits to print for branch lengths and ancestral character values.</dd>	<dt>format</dt>
<dd>a string indicating whether to output the result in simple Newick (i.e., <code>"phylip"</code>) or Nexus format.</dd>	<dt>...</dt>
<dd>additional arguments including <code>x</code>: a vector of character values, in which case ancestral states are estimated internally using <code>fastAnc</code>; and <code>CI</code>: a logical value indicating whether or not to estimate 95% confidence intervals.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.3-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Write a tree to file with ancestral states and (optionally) CIs at nodes — writeAncestors

<dl>

	<dt>tree</dt>
<dd>a phylogenetic tree or set of trees as an object of class <code>"phylo"</code> or <code>"multiPhylo"</code>.</dd>

	<dt>Anc</dt>
<dd>a vector of ancestral states, a list containing the ancestral states and 95% confidence intervals (as from <code>fastAnc</code> or <code>ace</code>, or a list of such results.</dd>

	<dt>file</dt>
<dd>an optional string with the filename for output.</dd>

	<dt>digits</dt>
<dd>an integer indicating the number of digits to print for branch lengths and ancestral character values.</dd>

	<dt>format</dt>
<dd>a string indicating whether to output the result in simple Newick (i.e., <code>"phylip"</code>) or Nexus format.</dd>

	<dt>...</dt>
<dd>additional arguments including <code>x</code>: a vector of character values, in which case ancestral states are estimated internally using <code>fastAnc</code>; and <code>CI</code>: a logical value indicating whether or not to estimate 95% confidence intervals.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

writeAncestors: Write a tree to file with ancestral states and (optionally) CIs at nodes

Description

Usage

Value

Arguments

Author

References

See Also