phytools (version 0.2-40)

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

Description

This function writes stochastic character mapped trees to file using the Newick style format of SIMMAP v1.0 (Bollback 2006). Note, can only write one tree at a time to file (hence the append option).

Usage

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

Arguments

tree

a phylogenetic tree as a modified object of class "phylo". See make.simmap and read.simmap.

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,"m

Value

• a file or string (if file=NULL).

References

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138. Bollback, J. P. 2006. Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

See Also

make.simmap, read.simmap, plotSimmap

Examples

# simulate a tree & data
	tree<-sim.history(pbtree(n=100,scale=1),Q=matrix(c(-1,1,1,-1),2,2))
	# generate stochastic character maps
	mtrees<-make.simmap(tree,tree$states,nsim=20)
	# write them to file
	lapply(mmtrees,write.simmap,file="treefile.tre",append=TRUE)