id.subtrees: id.subtrees

In iteRates: Parametric rate comparison

Description

This function identifies and numbers all subtrees within a tree of object class phylo. It creates the object required for function comp.fit.subs.

Usage

id.subtrees(tree)

Arguments

tree	A tree of object class phylo.

Details

This function identifies all the subtrees in a tree. These identifiers are used to identify the focal subtrees used in the comp.fit.subs function.

Value

A list that consists of the following:

tree	The original tree as object class phylo with nodes labeled identifying the identification number for all subtrees.
subtree	A list of all possible subtrees as object class phylo.

Note

This function will rename all node labels.

Author(s)

Premal Shah, Benjamin Fitzpatrick and James Fordyce.

References

Shah, P., B. M. Fitzpatrick, and J. A. Fordyce. 2013. A parametric method for assessing diversification rate variation in phylogenetic trees. Evolution 67:368-377.

See Also

comp.fit.subs

Examples

	## Not run: 
data(hivtree.newick)
cat(hivtree.newick, file = "hivtree.phy", sep = "\n") 
tree.hiv <- read.tree("hivtree.phy") # load tree 
unlink("hivtree.phy") # delete the file "hivtree.phy" 

idHIV<-id.subtrees(tree.hiv)
plot(idHIV$tree,show.node.label=TRUE)

## End(Not run)

iteRates documentation built on May 2, 2019, 9:12 a.m.