Aloha Gabriel, Joe and Graham have given you very good advice. I just wanted to chime in to reinforce the point that you should not apply a "phylogenetic correction" twice on the same set of data! If youʻve removed the expected covariance, it is good for an ordinary ANOVA. If you do a phylogenetic ANOVA that again accounts for phylogenetic covariance, you will INTRODUCE phylogenetic variance structure into your data. I really canʻt imagine a situation that would call for a double accounting of phylogenetic covariance.
If all youʻre doing is calculating shape variables, why not just take the ratio with size (SVL)? If it is a mass-dependent trait you can take the log-ratio with mass (you can divide by 3 if you like but at this point it is linear). Mass is ~ SVL^3, so you can come up with some rationale. Ratios are easily interpretable and are not evil, just make sure you donʻt have severe skew. Usually within a taxonomic group the range of variation is not that big, so you donʻt have a problem. Alternatively, you could create shape variables by pgls and then do an ordinary ANOVA. Alternatively, you could do OU models such as implemented in OUCH or OUwie or mvMorph. Option 1: pgls - residuals -> ordinary ANOVA Option 2: regression residuals or ratios -> phylogenetic ANOVA or OU methods Option 3: phylogenetic ancova, with size as a covariate. Marguerite On Thu, May 27, 2021 at 3:42 PM Graham Slater <[email protected]> wrote: > I might well be missing something but I think, Gabriel, that you do not > need to compute any residuals to do what you want to do. In your tail > length example, you perform a phylogenetic regression to get a > size-standardized tail length - in this case, the residuals of your pgls > model. That all makes sense because tail length is expected to vary as a > function of size but you're interested in the residual variation and > what explains that. I don't think you care about "correcting for > phylogeny" at this point in general terms though - you are only > including phylogeny to get the appropriate evolutionary regression for > tail~body size from which to compute tail length residuals. For your > ratio traits, there is (probably) no meaningful expectation of allometry > and so there is no need to do this. You can plug these variables > directly into a phylogenetic ANOVA or macroevolutionary model and > estimate the appropriate parameters. > > Regarding standard errors, most model-fitting functions (fitContinuous, > mvMorph, OUwie etc) allow you to include a measurement error term, which > just gets tacked on to the diagonals of the model-transformed > phylogenetic covariance matrix. It is good to do so, especially when > fitting OU models. Phylogenetic ANOVA (a la Garland et al.) uses > simulation to generate a null distribution of F-statistics to which the > result of an ordinary ANOVA is compared, so I don't see a > straightforward way of including standard errors there. A more direct > approach might be to use a phylogenetic Bayesian multi-level model, as > implemented in brms or mcmcglmm, where all observations are included and > species identity is treated as an effect. > > > I've probably missed something, but I hope this helps... > > > Graham > > -- > > Graham Slater [he/him/his] > Department of the Geophysical Sciences, University of Chicago > [email protected] > (773) 702 0249 > http://www.fourdimensionalbiology.com > > On 5/27/21 8:08 PM, Joe Felsenstein wrote: > > Gabriel Ferreira explained: > > > > > >> I will try to better explain my problem, and I really appreciate your > time > >> to help me with this issue. > >> My study is a conventional ecomorph with linear and univariate > >> measurements.... > >> > >> So... Some of my traits are linear measures that can and must be > >> "corrected" by body size, such as tail length. I usually conduct such > body > >> size corrections with phylogenetic regressions using *gls *func. from > >> *nlme*: > >> > > .... lots of details ... > > > > > >> So I could use the residuals of this regression in the phy ANOVAs ... > Does > >> it make sense? > >> > > > > Well, I am afraid I am lost. Perhaps someone else here could explain the > > issues to me ... > > > > > > Joe > > ------ > > Joe Felsenstein [email protected], [email protected] > > Department of Genome Sciences and Department of Biology, > > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > http://www.mail-archive.com/[email protected]/ > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > -- ____________________________________________ Marguerite A. Butler Professor Department of Biology 2538 McCarthy Mall, Edmondson Hall 216 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-4745 http://butlerlab.org http://manoa.hawaii.edu/biology/people/marguerite-butler http://www2.hawaii.edu/~mbutler [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
