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

Description Usage Arguments Value Author(s) References See Also

View source: R/write.simmap.R

Description

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

Usage

1
write.simmap(tree, file=NULL, append=FALSE, map.order=NULL, quiet=FALSE)

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.

Value

A file or string (if file=NULL).

Author(s)

Liam Revell liam.revell@umb.edu

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. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

make.simmap, read.simmap, plotSimmap


phytools documentation built on July 28, 2017, 9:01 a.m.