Hi Anna.
"1. I've tried implementing both phylogenetic ANOVA using aov.phylo
(Geiger package) and regular ANOVA test, and got the same results...."
See Garland et al. (1993). The phylogenetic ANOVA just fits a regular
ANOVA model & then generates a null distribution for the test statistic
(F) via numerical simulation on the tree.
"2. I've read some papers in which the authors used PGLS instead of
ANOVA in comparing two groups...."
This can be done. The assumption of (P)GLS is that the residual error in
y|x is multivariate normal with a distribution that ~vcv.phylo (i.e.,
the correlation of related species is proportional to their shared
fraction of time since the root), or some variant thereof (such as
Pagel's lambda model). This may apply even if x is a factor (although it
should probably be tested). E.g., see
http://blog.phytools.org/2013/02/a-comment-on-distribution-of-residuals.html
for more information.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/23/2013 12:59 PM, Anna Rice wrote:
Hello,
I'm relatively new to phylogeny analysis and have some questions.
Overall, my data consists of two groups and I'd like to compare ecological
attributes between these two groups. So here are my questions:
1. I've tried implementing both phylogenetic ANOVA using aov.phylo (Geiger
package) and regular ANOVA test, and got the same results. Do you have any
idea why this could happen?
my Phyl. ANOVA --> aov.phylo(attribute~category,phy,nsim=1000,test="Wilks")
my regular ANOVA --> aov(attribute~category,data=Data)
2. I've read some papers in which the authors used PGLS instead of ANOVA in
comparing two groups. What could be the reason for using PGLS when having a
categorical factor and not a continuous predictor factor?
Many thanks for your help,
Anna
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