Hi all -
Just a quick note to say that I tracked this down as a bug in GEIGER. The bug
is specific to using Wilks lambda for a MANOVA test statistic, and results
from the fact that the scale of Wilks lambda is reversed compared to other
test statistics (e.g. smaller values = more difference among groups).
I have updated geiger on github, and we will post this update to CRAN as soon
as we can. In the meantime, a fixed version of the function is pasted below.
Luke Harmon
aov.phylo=function(formula, phy, nsim=1000, test=c(Wilks, Pillai,
Hotelling-Lawley, Roy), ...){
xx=lapply(all.vars(formula), get)
flag='formula' must be of the form 'dat~group', where 'group' is a named
factor vector and 'dat' is a data matrix or named vector
if(!is.factor(xx[[2]])) stop(flag)
if(is.null(names(xx[[2]]))) stop(flag)
yy=merge(xx[[1]], xx[[2]], by=0)
if(nrow(yy)==0) stop(flag)
rownames(yy)=yy[,1]
yy=yy[,-1]
tmp-treedata(phy, yy, sort=TRUE)
phy=tmp$phy
yy=yy[phy$tip.label,]
group=structure(yy[,ncol(yy)], names=rownames(yy))
dat=as.matrix(yy[,-ncol(yy)])
rownames(dat)=rownames(yy)
s-ratematrix(phy, dat)
multivar=ifelse(ncol(dat)1, TRUE, FALSE)
if(multivar){
test=match.arg(test, c(Wilks, Pillai, Hotelling-Lawley, Roy))
m=summary.manova(mod-manova(dat~group), test=test)
f.data=m[[4]][1,2]
FUN=function(xx) summary.manova(manova(as.matrix(xx)~group),
test=test)[[4]][1,2]
sims-sim.char(phy, s, nsim=nsim)
f.null-apply(sims, 3, FUN)
out=as.data.frame(m[[4]])
attr(out, heading)=c(Multivariate Analysis of Variance
Table\n,Response: dat)
} else {
test=NULL
m=anova(mod-lm(dat~group))
f.data-m[1,4]
FUN=function(xx) anova(lm(xx~group))[1,4]
out=as.data.frame(m)
}
colnames(out)=gsub( , -, colnames(out))
sims-sim.char(phy, s, nsim=nsim)
f.null-apply(sims, 3, FUN)
if(test==Wilks) {
p.phylo = (sum(f.null f.data) + 1)/(nsim + 1)
} else {
p.phylo = (sum(f.null f.data) + 1)/(nsim + 1)
}
out$'Pr(phy)'=c(p.phylo, NA)
class(out) - c(anova, data.frame)
print(out, ...)
attr(mod, summary)=out
return(mod)
}
On Mar 6, 2014, at 11:54 AM, Anna Kostikova anna.kostik...@gmail.com wrote:
Absolutely agree, but typically such effect (at least in multiple regression)
could be a result of multicollinearity, that's why I still proposed to check
PCs to make sure there is nothing unusual about them.
Anna
On 6 Mar 2014, at 20:35, Paolo Piras paolo.pi...@uniroma3.it wrote:
PCscores coming from the same PCA are independent (orthogonal) by definition
best
paolo
Da: r-sig-phylo-boun...@r-project.org r-sig-phylo-boun...@r-project.org
per conto di Anna Kostikova anna.kostik...@gmail.com
Inviato: giovedì 6 marzo 2014 20.37
A: Frédérich Bruno
Cc: r-sig-phylo@r-project.org
Oggetto: Re: [R-sig-phylo] phylogenetic MANOVA
Hello Bruno,
Could you check how much your individual PCs are correlated with each other?
What you see might be a result of (high) multicollinearity (negative or
positive) between predictors.
Cheers,
Anna
On 6 Mar 2014, at 17:19, Frédérich Bruno bruno.freder...@ulg.ac.be wrote:
Dear All,
I am exploring body shape variation in a fish family, using shape variables
generated by landmark-based geometric morphometrics. To test shape
divergence among ecomorphs, I would like to perform a phylogenetic MANOVA.
To perform such a test, the function aov.phylo in geiger is available.
However, I think I have some troubles with it...
Indeed, firstly, I performed phylo ANOVAs using phylANOVA function in
phytools on the three first PCs (explaining more than 70% of shape
variation) of my shape dataset and found highly significant differences
among ecomorphs for PC2 and PC3.
Then, I applied a phylo MANOVA using aov.phylo including all the shape
variables and got a non-significant result (P-value = 1).
So, according to my expectations and the univariate results from
phylANOVAs, the results of phylo MANOVA seems a little bit strange to me...
Do someone have an explanation?
Do you know another function than aov.phylo to perform a phyloMANOVA? (for
comparisons)
Thank you in advance for your advices and your help!
Best,
Bruno
--
Dr. Bruno Frédérich
Postdoctoral Researcher F.R.S.-FNRS
Lab. of Functional and Evolutionary Morphology
University of Liège, Institut de Chimie (B6c)
4000 Liège, BELGIUM
Phone: 003243665133
Fax: 003243663715
E-mail: bruno.freder...@ulg.ac.be
Website: http://www2.ulg.ac.be/morfonct/
Open Repository and Bibliography (ORBi) http://orbi.ulg.ac.be/
Personal Publications (Open Access) http://tinyurl.com/Bruno-Reef
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