phylANOVA: Phylogenetic ANOVA and post-hoc tests

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Phylogenetic ANOVA and post-hoc tests

Description

Simulation based phylogenetic ANOVA following Garland et al. (1993), with post-hoc tests.

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.

Details

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).

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

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.

Author(s)

Liam Revell [e-mail]

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

anova, pairwise.t.test

phytools documentation built on Nov. 5, 2025, 5:11 p.m.