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

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Write a stochastic character mapped tree to file

Description

Writes one or multiple stochastic character mapped trees to file in several formats (following Bollback, 2006).

Usage

write.simmap(tree, file=NULL, append=FALSE, map.order=NULL, quiet=FALSE, 
    format="phylip", version=1.0)

Arguments

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

Value

A file.

Author(s)

Liam Revell [e-mail]

References

Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

make.simmap, read.simmap, plotSimmap

phytools documentation built on June 22, 2024, 10:39 a.m.