define.clade: Define clade
In PCPS: Principal Coordinates of Phylogenetic Structure

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/define.clade.R

Function to define groups (clades) in a phylogenetic tree.

1	define.clade(tree, threshold, time, method = c("threshold", "time"))

`tree`	Phylogenetic tree.
`threshold`	A threshold value to form the groups.
`time`	A cutting height (age) to form the groups.
`method`	Method to define the clades, "threshold" or "time".

In the method threshold the total length of phylogenetic tree is used as cutting factor. If threshold is near to zero the cutting is near the root, if threshold near to one cutting is near the tips.

The phylogenetic tree must contain the node labels for the function work. Use the makeNodeLabel for defining node labels in a flexible way.

`clades`	Tips and their clades.
`height`	The cutting height (age).

Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

makeNodeLabel

require(ape)	
tree<-makeNodeLabel(rcoal(10))
clades<-define.clade(tree, threshold = 0.8, method = "threshold")
clades
plot.phylo(tree, show.node.label = TRUE)
abline(v = clades$height)