Hello Sr, 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* : E.g. gls(trait X ~ body size, correlation=corPagel(1, phy=tree), data=data, method = "ML") Then after body size correction, I will use the residuals to conduct conventional ecomorphological hypotheses tests. At this part I will use functions that do not allow the inclusion of covariates (as far as I am aware of, that is why I need residuals), such as phylANOVA (from *phytools *package) and evolutionary trait model fitting from Butler and King (from *ouch * package). *I believe it worth mentioning that for these linear traits in particular, I won't include within species variation (SE in this case) because repeatability tests indicated high R values.* BUT... I have another set of traits that are ratios (or proportions), so it is independent of body size. Normally, I would use the log values of this proportion to directly conduct phylogenetic ANOVAs. But the problem is that repeatability tests indicated to be low for these proportions, therefore, I should consider somehow SE in the phy ANOVAs and evolutionary model fitting. My rationale was to use the same function of body size correction but instead of using body size as the predictor, I would fix the intercept at 1 and include SE in the weights argument, e.g. gls(trait X ~ 1, correlation=corPagel(1, phy=tree), data=data, method = "ML", weights= SE) WHERE SE <- varFixed (~1/sqrt(trait X SE)) So I could use the residuals of this regression in the phy ANOVAs ... Does it make sense? Thank you again! Gabriel Em qui., 27 de mai. de 2021 às 20:39, Joe Felsenstein <[email protected]> escreveu: > > If wants residuals of values of a trait in each species, taking into > account within-species variation and phylogeny, what does it mean if those > residuals correlate with those of some other character, or with an > environmental variable? > > Just asking which R machinery to use might wait until it is clear what the > intended task is and why that makes sense. > > 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 > > -- Gabriel Spanghero V. Ferreira Biólogo | Mestre em Biologia Comparada [[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]/
