hello everyone, in case it might be useful to anyone, there are a couple attempts at phylogenetic path analysis / structural equation modeling in the literature. I haven't looked closely at them and I'm not sure whether or where they are implemented, but perhaps others on the list might have more information:
Juan C. Santos and David C. Cannatella. 2011. Phenotypic integration emerges from aposematism and scale in poison frogs. PNAS 108(15) 6175-6180 http://www.pnas.org/content/108/15/6175.full Juan C. Santos. The implementation of phylogenetic structural equation modeling for biological data from variance-covariance matrices, phylogenies, and comparative analyses. (Thesis) http://repositories.lib.utexas.edu/handle/2152/ETD-UT-2009-12-459 Achaz von Hardenberg and Alejandro Gonzalez-Voyer. 2013. Disentangling evolutionary cause-effect relationships with phylogenetic confirmatory path analysis. Evolution 67(2) 378-387 http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01790.x/abstract HTH Abraços, Rafael Maia --- http://www.rafaelmaia.net/ PhD Candidate, Integrated Bioscience University of Akron "A little learning is a dangerous thing; drink deep, or taste not the Pierian spring." (A. Pope) On Jul 14, 2013, at 6:25 AM, Theodore Garland Jr <theodore.garl...@ucr.edu> wrote: > "Maybe what we need here is an approach based on > simultaneous equations (aka structural equation models), but I'm not > aware whether this exists in a phylogenetic framework." > > Exactly! And it will need to incorporate "measurement error" in all > variables as well as, eventually, uncertainly in the phylogenetic topology > and branch lengths. > > Good luck, > Ted > > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Emmanuel Paradis [emmanuel.para...@ird.fr] > Sent: Sunday, July 14, 2013 3:18 AM > To: Joe Felsenstein > Cc: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] PGLS vs lm > > Hi all, > > I would like to react a bit on this issue. > > Probably one problem is that the distinction "correlation vs. > regression" is not the same for independent data and for phylogenetic data. > > Consider the case of independent observations first. Suppose we are > interested in the relationship y = b x + a, where x is an environmental > variable, say latitude. We can get estimates of b and a by moving to 10 > well-chosen locations, sampling 10 observations of y (they are > independent) and analyse the 100 data points with OLS. Here we cannot > say anything about the correlation between x and y because we controlled > the distribution of x. In practice, even if x is not controlled, this > approach is still valid as long as the observations are independent. > > With phylogenetic data, x is not controlled if it is measured "on the > species" -- in other words it's an evolving trait (or intrinsic > variable). x may be controlled if it is measured "outside the species" > (extrinsic variable) such as latitude. So the case of using regression > or correlation is not the same than above. Combining intrinsic and > extinsic variables has generated a lot of debate in the literature. > > I don't think it's a problem of using a method and not another, but > rather to use a method keeping in mind what it does (and its > assumptions). Apparently, Hansen and Bartoszek consider a range of > models including regression models where, by contrast to GLS, the > evolution of the predictors is modelled explicitly. > > If we want to progress in our knowledge on how evolution works, I think > we have to not limit ourselves to assess whether there is a > relationship, but to test more complex models. The case presented by Tom > is particularly relevant here (at least to me): testing whether group > size affects brain size or the opposite (or both) is an important > question. There's been also a lot of debate whether comparative data can > answer this question. Maybe what we need here is an approach based on > simultaneous equations (aka structural equation models), but I'm not > aware whether this exists in a phylogenetic framework. The approach by > Hansen and Bartoszek could be a step in this direction. > > Best, > > Emmanuel > > Le 13/07/2013 02:59, Joe Felsenstein a écrit : >> >> Tom Schoenemann asked me: >> >>> With respect to your crankiness, is this the paper by Hansen that you are >>> referring to?: >>> >>> Bartoszek, K., Pienaar, J., Mostad, P., Andersson, S., & Hansen, T. F. >>> (2012). A phylogenetic comparative method for studying multivariate >>> adaptation. Journal of Theoretical Biology, 314(0), 204-215. >>> >>> I wrote Bartoszek to see if I could get his R code to try the method >>> mentioned in there. If I can figure out how to apply it to my data, that >>> will be great. I agree that it is clearly a mistake to assume one variable >>> is responding evolutionarily only to the current value of the other >>> (predictor variables). >> >> I'm glad to hear that *somebody* here thinks it is a mistake (because it >> really is). I keep mentioning it here, and Hansen has published extensively >> on it, but everyone keeps saying "Well, my friend used it, and he got >> tenure, so it must be OK". >> >> The paper I saw was this one: >> >> Hansen, Thomas F & Bartoszek, Krzysztof (2012). Interpreting the >> evolutionary regression: The interplay between observational and biological >> errors in phylogenetic comparative studies. Systematic Biology 61 (3): >> 413-425. ISSN 1063-5157. >> >> J.F. >> ---- >> Joe Felsenstein j...@gs.washington.edu >> Department of Genome Sciences and Department of Biology, >> University of Washington, Box 355065, Seattle, WA 98195-5065 USA >> >> _______________________________________________ >> 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/ >> > > _______________________________________________ > 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/ > > _______________________________________________ > 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/ _______________________________________________ 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/
