People, many thanks for keeping this list so functional. Sorry for the
slow reply, had a small accident, but is ok now. I'll answer Liam
first and Ted and Brian in sequence.
Liam, yes, the error is fatal, and the BrownieREML worked. But seems
it did not converged:
These are the results:
brownieREML(tree,data[,Area_Km2],maxit=2000)$sig2.single
[1] 6.444619e+12
$logL1
[1] -135.4347
$sig2.multiple
2
4.911978e+12
$logL2
[1] -135.6168
$convergence
[1] FALSE
Also tried the Ouwie option, but then I needed to generate a
simmap.tree. Tried with make.simmap but the help tells me it only
works for discrete data, and my response variable is continuous. To be
more informative, I pasted below a very small graph of the uncorrected
relationship I want to analyze using phylogenetic methods.
Ted and Brian, thanks for you advice and references on number of species.
Im comparing nearly all known syntopic species of two sister clades with
different morphs. I know thats inappropriate for inferring adaptation and
for estimating several parameters from such a low number of species.
However, I expected to be able to reliably recover the differences between
the two groups and the degree to which phylogeny was explaining the
relationships.
However, for this case, as my data are highly heteroskedastic (see graph
below) and the differences between the treatments is related to the maximum
value that the response variable attains, do you think that adding a
outgroup and performing a Bartlets test over phylogenetic contrasts would
at least make a honest test of the relationship?
Agus
[image: Imágenes integradas 1]
2012/9/18 Theodore Garland Jr theodore.garl...@ucr.edu
That number of 20 comes up from the simulations provided by both of these
papers:
Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
phylogenetic signal in comparative data: behavioral traits are more labile.
Evolution 57:717-745.
Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis
and comparative data: a test and review of evidence. Am. Nat. 160:712-726.
Note, however, that both of those sets of simulations assumed no
measurement error in the phenotypic trait(s) and no error in the
phylogenetic topology or branch lengths. Hence, they may well have
underestimated how many species you need in the real world! As they say,
your mileage may vary ...
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 Brian O'Meara [bome...@utk.edu]
Sent: Tuesday, September 18, 2012 1:25 PM
To: Agus Camacho
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] variation in rates over time, unexpected
message when using Brownie.lite
That's a fairly small tree to be doing this with -- an old rule of thumb (I
think from Pagel) is 20 tips per parameter. Common issues are zero length
(or effectively zero length) branch lengths (what is min(phy$edge.length)?)
and polytomies (methodologically not a problem, but many packages don't
deal well with these).
Brian
___
Brian O'Meara
Assistant Professor
Dept. of Ecology Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara
On Tue, Sep 18, 2012 at 4:08 PM, Agus Camacho agus.cama...@gmail.com
wrote:
Dear all, I tried to test something similar to Jason, but relating the
change in rates to the acquisition of a trait, instead to a specific
date.
For that, I used a phylogeny with ten taxa, without outgroup.
I used exactly the same script gently proposed by Liam but got the
following error message:
Error in solve.default(model1$hessian) :Lapack routine dgesv: system is
exactly singular
I've been looking through the internet but was not able to identify what
causes this error. Any hint about that?
BTW, anybody knows how to directly answer a message found in the digest
of
the mail list, without leaving the thread?
Below, I pasted the complete thread dealing with this topic.
Cheers,
Agus
Message: 9
Date: Tue, 18 Sep 2012 00:13:00 -0400
From: Brian O'Meara bome...@utk.edu
To: Jason
