define.clade: Define clade

In PCPS: Principal Coordinates of Phylogenetic Structure

Define clade

Description

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

Usage

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

Arguments

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".

Details

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.

Value

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

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

See Also

makeNodeLabel

Examples

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)

PCPS documentation built on June 18, 2026, 1:07 a.m.