Cecile, Peter, Joe and all- As far as I understand, Peter's analysis involves paleontological data with non-ultrametric trees, and based on my understanding of Slater (2014), the Freckleton approach using PIC is invalid for that type of dataset, although Fitzjohn's pruning algorithm might still apply.
http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12201/abstract Cheers, -Dave On Mon, Dec 22, 2014 at 10:15 AM, Cecile Ane <a...@stat.wisc.edu> wrote: > > Hi again Peter, > > If matrix inversion and determinants are a bottleneck, there are multiple > ways to avoid them (without assigning random effects to ancestral species), > including Felsenstein (1973), FitzJohn (2012) and Freckleton (2012). The > speed-up is huge if you have thousands of tips. This algorithm extends to a > variety of models: > http://sysbio.oxfordjournals.org/cgi/reprint/syu005?ijkey= > bIsHxa2dpqXCplc&keytype=ref > > Cecile. > > On 12/22/2014 12:01 PM, Peter Smits wrote: > >> Cecile and Joe, >> >> Thank you for the replies. That helped clear up a lot for me. >> >> And thank you for the link Cecile. Estimating sigma_phy is quite a pain >> because of all the matrix inversions. I've a tree of approx. 2000 tips, >> so even using of a Cholesky decomposed V_{phy} doesn't buy me much time >> at all. >> >> Because the vector of means for the MVN in my work is all 0s, I've >> written my own MVN sampler to try and minimize how many inversions or >> determinants need to be calculated. The stan mailing list had a great >> little discussion on how to speed up estimation of MVN random effects >> with partially known covariance matrices >> https://groups.google.com/forum/#!topic/stan-users/HcvYaDu71_Y and I >> just followed that code. Now my posterior sampling at least gets off the >> ground and finishes. >> >> The stan list discussion possibly provides a useful starting template >> for other people on this list trying to do similar things. >> >> Cheers, >> >> Peter >> >> On Mon, Dec 22, 2014 at 11:32 AM, Cecile Ane <a...@stat.wisc.edu> wrote: >> >> Hi Peter, >> >> We have taken a similar approach in this paper: >> http://onlinelibrary.wiley.__com/doi/10.1111/evo.12582/__abstract >> >> <http://onlinelibrary.wiley.com/doi/10.1111/evo.12582/abstract> >> We also use a Bayesian approach, with a prior that allows us to >> integrate the ancestral state and the total variance analytically >> (no need for MCMC for those parameters). Our notation for your >> sigma_phy is lambda, like Pagel's, and we do use multiple >> individuals per species. For what it's worth. >> >> Regarding the scaling of branch lengths, I agree with Joe that there >> is nothing particular about 1, other than providing an easier >> interpretation for the numerical value of the phylogenetic variance. >> Cheers, >> Cecile. >> >> >> On 12/14/2014 01:03 PM, Peter Smits wrote: >> >> Hi list, >> >> I have a similar question to Edwin. I too am working with a >> hierarchical >> Bayesian model, though I've implemented it in stan. I've included >> a >> phylogenetic random effect term, which is modeled as being >> distributed as >> multivariate normal with known covariance matrix up to a constant, >> sigma_{phy}. This follows Lynch '91 Am Nat and Housworth et al. >> '04 Am Nat >> by drawing on the similarity with the "animal model" from >> quantitative >> genetics. >> >> My question is about the scaling of the covariance matrix: is it >> necessary >> to have the the diagonal terms satisfy x <= 1 and all the off >> diagonals to >> be 0 <= x < 1? I have a time scaled phylogeny from which I have my >> covariance matrix, so currently all elements of the matrix are >> not scaled >> so that the greatest distance from the root to a tip is 1. >> Currently, the >> elements of the matrix are just the sum of the shared branch >> lengths. Is >> this appropriate? Why or why not? >> >> Any input would be much appreciated. >> >> Cheers, >> >> Peter Smits >> -- >> Peter D Smits >> Grad student >> Committee on Evolutionary Biology >> University of Chicago >> psm...@uchicago.edu <mailto:psm...@uchicago.edu> >> http://home.uchicago.edu/~psmits/home.html >> > > -- > Cecile Ane > Departments of Statistics and of Botany > University of Wisconsin - Madison > www.stat.wisc.edu/~ane/ > > CALS statistical consulting lab: > www.cals.wisc.edu/calslab/stat_consulting.php > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
