write.simmap {phytools} | R Documentation |
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).
write.simmap(tree, file=NULL, append=FALSE, map.order=NULL)
tree |
a phylogenetic tree as a modified object of class |
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, |
A file or string (if file=NULL
).
Liam Revell liam.revell@umb.edu
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.
make.simmap
, read.simmap
, plotSimmap
# 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 ## Not run: lapply(mmtrees,write.simmap,file="treefile.tre",append=TRUE) ## End(Not run)