psc: Phylogenetic serial contrasts

In FabioLugar/mvEvol: Tools For Evolutionary Morphology and Morphometrics

Phylogenetic serial contrasts

Description

Calculate McPeek's phylogenetic contrasts along all branches of a phylogeny

Usage

psc(x, phy, scale = TRUE)

Arguments

x	a numeric vector.
phy	an object of class "phylo"
scale	if contrasts should be scaled by expected variance. Default is TRUE

Details

Sequential contrasts are calculated along the branches of the phylogeny, instead of being calculated at each node, like standard Phylogenetic Independent Contrasts (Felsenstein, 1985). Like PIC, these contrasts can be scaled by expected variance and are a localized measure of evolutionary rates. These contrasts where first proposed by McPeek (1995) to find branches on a phylogeny where rates of evolution where higher.

Value

A vector of phylogenetically sequential contrasts. Vector contains one entry for each branch of the tree on the order that they appear on the phylo object (cladewise order. See reorder.phylo).

Author(s)

Fabio Andrade Machado

References

McPeek, M. 1995. "Testing Hypotheses About Evolutionary Change on Single Branches of a Phylogeny Using Evolutionary Contrasts". The American Naturalist 145(5):686–703.

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

See Also

pic

FabioLugar/mvEvol documentation built on Dec. 21, 2024, 7:25 p.m.