geiger (version 1.2-13)

phy.anova: Phylogenetic ANOVA and MANOVA

Description

Calculates ANOVA or MANOVA, and returns p-value based on Brownian motion simulations

Usage

phy.anova(phy, data, group, data.names=NULL, nsim=1000)
phy.manova(phy, data, group, data.names=NULL, nsim=1000, test="Wilks")

Arguments

phy

an object of class 'phylo'

data

Dependent variable(s) - should be continuous

group

Independent variable - should be a factor

data.names

Taxon names in order, corresponding to x and group; not needed if data has names stored as 'names' or 'rownames'

nsim

Number of simulations for calculating p-value; default = 1000

test

If you're using a MANOVA, the name of the test statistic to be used. Partial matching is used so the name can be abbreviated. Options are "Pillai", "Wilks", "Hotelling-Lawley", and "Roy"

Value

• Standard ANOVA or MANOVA table and p-value based on simulations

Details

This function allows an ANOVA or MANOVA in a phylogenetic context. First, the test statistic for ANOVA (one dependent variable) or MANOVA (more than one dependent variable) is calculated. The null distribution of this test statistic is then obtained by simulating new sets of dependent variables on the phylogenetic tree. Simulations are run under a Brownian motion model. For ANOVA, the rate parameter is estimated from the average squared independent contrast; for MANOVA the simulations use an estimated variance-covariance (vcv) matrix from the GEIGER function ic.sigma.

For MANOVA, you can specify the test statistic for the summary table. Wilks' statistic is most popular in the literature; for more details see the summary.manova help page.

References

Garland Jr., T., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Syst. Biol. 42(3):265-292.

See Also

anova, summary.manova, ic.sigma

Examples

data(geospiza)
attach(geospiza)


f<-as.factor(c(rep(0, 7), rep(1, 6)))


phy.manova(geospiza.tree, geospiza.data, f)

x<-geospiza.data[,1]

phy.anova(geospiza.tree, x, f, data.names=rownames(geospiza.data))