phylANOVA {phytools} | R Documentation |
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).
phylANOVA(tree, x, y, nsim=1000, posthoc=TRUE, p.adj="holm")
tree |
a phylogenetic tree in |
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 |
Uses a little bit of code from phy.anova
in the "geiger" package as well as pairwise.t.test
.
A list 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. |
Liam Revell liam.revell@umb.edu
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.