write.nexus.simmap: Write phylo4d_ext object or list to a nexus file

In phyext: An extension of some of the classes in phylobase. Tree objects now support subnodes on branches

Description

This function is similar to write.nexus from the ape package. If the there are subnodes in the object then these are written as SIMMAP-formatted (v1.0) strings.

Usage

write.nexus.simmap(obj, file = "", translate = TRUE, ...)

Arguments

obj	A phylo4d_ext object or list of these objects
file	The file to output to
translate	Should taxa names be translated (not written in every newick string) or not.
...	Other arguments which are passed to write.simmap

Details

This function will eventually support more subnode output formats other than just SIMMAP v1.0. Work is in progress on this. But for now, that is the only format that the brownie core reads and this function was written mainly to generate brownie files.

It borrows a lot of it's code and structure from the ape function write.nexus

Value

Nothing

Author(s)

J. Conrad Stack

See Also

read.nexus.simmap, write.simmap

phyext documentation built on May 2, 2019, 5:19 p.m.