[R-sig-phylo] pPCA - global and local components

[Franck Stefani]

Dear Theodore,

Thanks for your reply but I fear I am not skilled enough in stats for
considering your alternative... I have a look at the paper published by
Jombart et al. (2010, Putting phylogeny into the analysis of biological
traits: a methodological approach. J Theor Biol 264: 693) and it seems they
have only considered  the first global and/or first local components and
this even if the second global or local components seemed to explain a
certain amount of the total variance.

Franck


2012/8/23 Theodore Garland Jr theodore.garl...@ucr.edu

 That seems like it would be OK, at least if you think it is OK for
 nonphylogenetic PCA.
 An alternative is to simulate data along your phylogeny, analyze it the
 same way, do it a couple thousand times, then make an empirical null
 distribution of, say, the eigenvalues when the data have no correlation on
 average but increased variance in the values of correlations caused by the
 phylogenetic hierarchy.
 This is discussed in our very old PHYLOGR package.
 However, you will need to make some decisions about the branch lengths
 to use for your individuals within species, represented by a bunch of
 mini-star phylogenies.

 Cheers,
 Ted

 Theodore Garland, Jr.
 Professor
 Department of Biology
 University of California, Riverside
 Riverside, CA 92521
 Office Phone:  (951) 827-3524
 Facsimile:  (951) 827-4286 = Dept. office (not confidential)
 Email:  tgarl...@ucr.edu
 http://www.biology.ucr.edu/people/faculty/Garland.html
 http://scholar.google.com/citations?hl=enuser=iSSbrhwJ

 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 Franck Stefani [fopstef...@gmail.com]
 Sent: Wednesday, August 22, 2012 3:50 PM
 To: r-sig-phylo@r-project.org
 Subject: [R-sig-phylo] pPCA - global and local components

 Hi,

 Among the graphical outputs of the pPCA, there is the scree plot showing
 the global and local components. I would like to know what are the criteria
 to define the number of GPC or LPC to interpret ? Can we use a broken stick
 model?

 Cheers,

 Franck

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[R-sig-phylo] ppca

[franck STEFANI]

Hi,
I am using the ppca for assessing which trait or which combination of
traits are the most usefull for discriminating species. I have got a
phenetic data set of 52 traits for 76 individuals representing 32 species +
a seven loci molecular data set.
I have got multiple individuals per species but I have noticed in the data
sets that are provided with the package adephylo and in the recent
publications that have used the ppca that the data sets do not have
multiple indviduals per species.
I wonder if it is important to reduce the phenetic data set to a single
value for each species for correctly running the ppca. If so, would you
suggest to randomly choose one value for one specimen per species or to
calculate the average for all the individuals per species?

Franck

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