pic3 {picante}R Documentation

Independent contrasts

Description

Modification of pic function from ape to return internal node values as well as contrasts and variance of contrasts.

Usage

pic3(x, phy, scaled = TRUE, var.contrasts = TRUE)

Arguments

x Trait vector (same order as phy$tip.label)
phy phylo object
scaled TRUE = standardize contrasts by branch lengths
var.contrasts TRUE = return variance of contrasts

Value

Matrix with three columns:

row.names node numbers
contrasts independent contrast value
variance variance of contrasts (sum of subtending branch lengths)
node.vals values calculated at internal nodes by contrast algorithm

Warning

Assumes that trait data are sorted in the same order as phylo$tip.label

Author(s)

Original pic function by Emmanuel Paradis <Emmanuel.Paradis@mpl.ird.fr> modified to return node.vals by David Ackerly <dackerly@berkeley.edu>

References

Felsenstein J (1985) Phylogenies and the comparative method. American Naturalist 125: 1-15.

Garland T, Jr, Harvey PH & Ives AR (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41: 18-32.

See Also

pic

Examples

randtree <- rcoal(20)
randtraits <- evolve.brownian(randtree)
pic3(randtraits,randtree)

[Package picante version 0.7-2 Index]