phylogenetic ANOVA and MANOVA
computing phylogenetic ANOVA or MANOVA
a formula specifying the model (see Examples)
a phylogenetic tree of class 'phylo'
number of simulations to run
test statistic to apply if MANOVA
additional arguments to be passed to
This function performs 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
For MANOVA, you can specify the test statistic for the summary table. Wilks' statistic is most popular in the
literature and for further details, see
The function prints (and returns) a standard ANOVA or MANOVA table and p-value based on simulations (from the
Pr(phy) column). For convenience, the summary table is included as an attribute of the returned object (see Examples).
JM Eastman and LJ Harmon
Garland T Jr, AW Dickerman, CM Janis, and JA Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42(3):265-292.
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