write.simmap: 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).

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

A file.

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.

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.