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

This function writes stochastic character mapped trees to file using the Newick style format of SIMMAP v1.0 (Bollback 2006).

phylogenetics

comparative method

input/output

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which 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, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or 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.

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

Description

Usage

Arguments

Value

References

See Also