write.simmap

an object of class <code>"simmap"</code> or <code>"multiSimmap"</code>.

tree

file

a logical value indicating whether to append to file.

append

a optional value specifying whether to write the map in left-to-right or right-to-left order. Acceptable values are "left-to-right" or "right-to-left" or some abbreviation of either. If not provided, <code>write.simmap</code> will use <code>attr(tree,"map.order")</code> if available.

map.order

logical value indicating whether or not to print a warning message when <code>map.order</code> is neither specified by a function argument or as an attribute of <code>tree</code>.

quiet

format

version of SIMMAP. Note that the options are <code>1.0</code> and <code>1.5</code>. <code>version=1.5</code> is generally recommended because in this format the tree can also be parsed by typical tree readers, but absent its mapped trait.

version

This function writes stochastic character mapped trees to file in multiple SIMMAP formats (Bollback 2006).

phylogenetics

comparative method

input/output

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, 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 data, for continuous, discrete, and multivariate characters. 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 phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety 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)

write.simmap function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code> or <code>"multiSimmap"</code>.</dd>	<dt>file</dt>
<dd>an optional filename.</dd>	<dt>append</dt>
<dd>a logical value indicating whether to append to file.</dd>	<dt>map.order</dt>
<dd>a optional value specifying whether to write the map in left-to-right or right-to-left order. Acceptable values are "left-to-right" or "right-to-left" or some abbreviation of either. If not provided, <code>write.simmap</code> will use <code>attr(tree,"map.order")</code> if available.</dd>	<dt>quiet</dt>
<dd>logical value indicating whether or not to print a warning message when <code>map.order</code> is neither specified by a function argument or as an attribute of <code>tree</code>.</dd>	<dt>format</dt>
<dd>file format for output.</dd>	<dt>version</dt>
<dd>version of SIMMAP. Note that the options are <code>1.0</code> and <code>1.5</code>. <code>version=1.5</code> is generally recommended because in this format the tree can also be parsed by typical tree readers, but absent its mapped trait.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.0-3" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Write a stochastic character mapped tree to file — write.simmap

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"simmap"</code> or <code>"multiSimmap"</code>.</dd>

	<dt>file</dt>
<dd>an optional filename.</dd>

	<dt>append</dt>
<dd>a logical value indicating whether to append to file.</dd>

	<dt>map.order</dt>
<dd>a optional value specifying whether to write the map in left-to-right or right-to-left order. Acceptable values are "left-to-right" or "right-to-left" or some abbreviation of either. If not provided, <code>write.simmap</code> will use <code>attr(tree,"map.order")</code> if available.</dd>

	<dt>quiet</dt>
<dd>logical value indicating whether or not to print a warning message when <code>map.order</code> is neither specified by a function argument or as an attribute of <code>tree</code>.</dd>

	<dt>format</dt>
<dd>file format for output.</dd>

	<dt>version</dt>
<dd>version of SIMMAP. Note that the options are <code>1.0</code> and <code>1.5</code>. <code>version=1.5</code> is generally recommended because in this format the tree can also be parsed by typical tree readers, but absent its mapped trait.</dd>

</dl>

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

write.simmap: Write a stochastic character mapped tree to file

Description

Usage

Value

Arguments

Author

References

See Also