Phylogenetic MANOVA in R? [closed]

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Does anyone know of a package or method in R of carrying out a MANOVA whilst controlling for phylogenetic non-independence?

Thank you!

Answer 1

sos package is your friend:

library('sos')
findFn('phylogenetic MANOVA')

seems like geiger package and more precisely aov.phylo performs phylogenetic ANOVA or MANOVA.

Here an example from the help :

library(geiger)
geo=get(data(geospiza))
dat=geo$dat
d1=dat[,1]
grp<-as.factor(c(rep(0, 7), rep(1, 6)))
names(grp)=rownames(dat)

## MANOVA
x=aov.phylo(dat~grp, geo$phy, nsim=50, test="Wilks")
Multivariate Analysis of Variance Table

Response: dat
          Df   Wilks approx-F num-Df den-Df   Pr(>F) Pr(phy)
group      1 0.27872   3.6229      5      7 0.061584   0.549
Residuals 11