"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/
