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phytools (version 0.7-20)

phylANOVA: Phylogenetic ANOVA and post-hoc tests

Description

This function performs the simulation-based phylogenetic ANOVA of Garland et al. (1993) and (optionally) conducts all posthoc comparisons of means among groups (also obtaining the P-values by phylogenetic simulation).

Usage

phylANOVA(tree, x, y, nsim=1000, posthoc=TRUE, p.adj="holm")

Arguments

tree

a phylogenetic tree in "phylo" format.

x

a vector containing the groups.

y

a vector containing the response variable (continuously valued).

nsim

an integer specifying the number of simulations (including the observed data).

posthoc

a logical value indicating whether or not to conduct posthoc tests to compare the mean among groups.

p.adj

method to adjust P-values for the posthoc tests to account for multiple testing. Options same as p.adjust.

Value

An object of class "phylANOVA" containing the following elements:

F

F from observed data.

Pf

P-value for F from simulation.

T

matrix of t-values.

Pt

matrix of multiple test corrected P-values from posthoc t-tests.

Details

This function uses a little bit of code from both phy.anova in the geiger package and pairwise.t.test.

References

Garland, T., Jr., A. W. Dickerman, C. M. Janis, & J. A. Jones. (1993) Phylogenetic analysis of covariance by computer simulation. Systematic Biology, 42, 265-292.

Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, W. Challenger. (2008) GEIGER: investigating evolutionary radiations. Bioinformatics, 24, 129-131.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

anova, pairwise.t.test