Re: [R-sig-phylo] nonparametric PGLS

2012-05-11 Thread Emmanuel Paradis 

Hi Pascal,

The assumption of normality in GLS, as in OLS, concerns the residuals 
not the data. A recent reference on this issue is:


Alain F. Zuur, Elena N. Ieno and Chris S. Elphick: A protocol for data 
exploration to avoid common statistical problems. Methods in Ecology  
Evolution 2010, 1, 3–14. doi: 10./j.2041-210X.2009.1.x


To answer your specific question, I'm not aware of such nonparametric 
method though a Monte Carlo procedure might be feasible.


Best,

Emmanuel

Pascal Title wrote on 11/05/2012 10:46:

Hi everyone

I have character data for species on a phylogeny, but simple
transformations like log-transformations or square-root transformations are
not proving to be sufficient to get the data to be normal. If this were a
non-phylogenetic test, I would resort to something like a Spearman
correlation, which is non-parametric.
But with phylogenetic generalized least squares, is there any method that
is nonparametric?

Thanks!


-Pascal Title

--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/

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Re: [R-sig-phylo] nonparametric PGLS

2012-05-11 Thread Theodore Garland Jr 
I general, you should not be worrying about normality of the tip data, but 
rather the residuals of whatever multiple regression-type model you are 
implementing.  Check those, and maybe they will be OK with a particular 
combination of independent variables.  Bad residuals can adversely affect the 
likelihood of a model, so particularly check for big outliers.

Cheers,
Ted

Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone:  (951) 827-3524
Wet Lab Phone:  (951) 827-5724
Dry Lab Phone:  (951) 827-4026
Home Phone:  (951) 328-0820
Facsimile:  (951) 827-4286 = Dept. office (not confidential)
Email:  tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html

Experimental Evolution: Concepts, Methods, and Applications of Selection 
Experiments. 2009.
Edited by Theodore Garland, Jr. and Michael R. Rose
http://www.ucpress.edu/book.php?isbn=9780520261808
(PDFs of chapters are available from me or from the individual authors)


From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on 
behalf of Pascal Title [pascalti...@gmail.com]
Sent: Thursday, May 10, 2012 8:46 PM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] nonparametric PGLS

Hi everyone

I have character data for species on a phylogeny, but simple
transformations like log-transformations or square-root transformations are
not proving to be sufficient to get the data to be normal. If this were a
non-phylogenetic test, I would resort to something like a Spearman
correlation, which is non-parametric.
But with phylogenetic generalized least squares, is there any method that
is nonparametric?

Thanks!


-Pascal Title

[[alternative HTML version deleted]]

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[R-sig-phylo] nonparametric PGLS

2012-05-10 Thread Pascal Title 
Hi everyone

I have character data for species on a phylogeny, but simple
transformations like log-transformations or square-root transformations are
not proving to be sufficient to get the data to be normal. If this were a
non-phylogenetic test, I would resort to something like a Spearman
correlation, which is non-parametric.
But with phylogenetic generalized least squares, is there any method that
is nonparametric?

Thanks!


-Pascal Title

[[alternative HTML version deleted]]

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