Hi Sergio, If what you want to do is to partition your morphometric data into size and shape components, then you can use Mosimann’s methods which do not require regressions or phylogenetic corrections.
Mosimann, J. E. 1970. Size allometry: size and shape variables with charac- terization of the lognormal and generalized gamma distributions. J. Am. Stat. Assoc. 65:930–945. Mosimann, J. E., and F. C. James. 1979. New statistical methods for allometry with application to Florida red-winged blackbirds. Evolution 33:444– 459. here is how I used them: Claramunt, S. (2010). Discovering exceptional diversifications at continental scales: the case of the endemic families of Neotropical suboscine passerines. Evolution, 64(7), 2004-2019. Cheers, Santiago On Jun 18, 2015, at 11:55 AM, Sergio Ferreira Cardoso <sff.card...@campus.fct.unl.pt> wrote: > Hi Liam, > > Again, thank you for the answer. Yes, I'm aware that they are > phylogenetically correlated and that they need to be subsequently analysed > with methods such as PGLS. In fact, when I apply a normality test to ( > chol(solve(vcv(tree)))%*%residuals(fit))the "transformed residuals" are > normally distributed. But I understand that the residuals I need to use as > size-corrected traits are the ones without the transformation (that, in my > case, aren't normal, and that's why I was a bit worried). > Thanks a lot for the help. > > Cheers, > Sérgio. > > 2015-06-18 15:54 GMT+01:00 Liam J. Revell <liam.rev...@umb.edu>: > >> Hi Sérgio. >> >> What Simon (& I, in my blog post) suggested is that to test the 'normality >> assumption' you need to first transform the residuals with the inverse >> Cholesky decomposite matrix. This will give you a vector in which the >> values should be normal & independent (assuming that the correlation >> structure of the residuals is properly given by the tree). However these >> values are no longer associated with species(!) so they cannot be used in >> subsequent among-species analyses. So, basically, yes - you should use the >> residuals before transformation in cross-species analyses (for instance, as >> 'size corrected' trait values); however you need to remember that they are >> still phylogenetically correlated. I hope that's clear enough. >> >> All the best, Liam >> >> Liam J. Revell, Assistant Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> On 6/18/2015 6:16 AM, Sergio Ferreira Cardoso wrote: >> >>> Hello again, >>> >>> Thanks for your help. This kind of solved my problem. I normally use >>> some kind of test (shapiro or komolgorov) to test for normality. I know >>> histograms or qqnorm plots a more helpful, but they are more >>> "vulnerable" to each others interpretation. >>> So, just to make clear one thing: these kind of analysis of the residual >>> error >>> ( >>> http://blog.phytools.org/2013/02/a-comment-on-distribution-of-residuals.html >>> ) >>> has nothing to do with phylogenetic residuals taken from a regression >>> (in order to obtain relative values - size-correction as in Revell, L. >>> J. (2009). Size‐correction and principal components for interspecific >>> comparative studies. Evolution, 63(12), 3258-3268.). So even if >>> residuals from a PGLS aren't normal, this means I can still use them as >>> size-corrected values for a certain trait, correct? >>> Once again, thank you very much for your advices. >>> >>> Best regards, >>> Sérgio. >>> >>> 2015-06-18 4:56 GMT+01:00 Simon Blomberg <s.blombe...@uq.edu.au >>> <mailto:s.blombe...@uq.edu.au>>: >>> >>> >>> Hi Sérgio. >>> >>> Liam is right. But we do expect the normalised residuals to be >>> approximately Normal. You can calculate the normalised residuals by >>> pre-multiplying the raw residuals by the inverse of the Cholesky >>> decomposition of the phylogenetic variance-covariance matrix, and >>> then dividing by the estimate of the residual standard deviation (ie >>> sigma). You may have to plug in a value for any parameters that are >>> co-estimated along with the regression (Pagel's lambda, etc.). If >>> you use the gls function in the nlme package to fit your model, then >>> it's all easy: >>> >>> fit <- gls(response~explanatory, correlation=corPagel(1, >>> phy=my.tree), data=dat)) >>> res <- residuals(fit, type="normalized") >>> >>> Then you can do some test for normality on those (I don't ordinarily >>> recommend such things, although >>> SnowsPenultimateNormalityTest in the TeachingDemos package is the >>> best I have seen). More usefully, you can do a normal >>> quantile-quantile plot to graphically see whether your normalised >>> residuals are normal enough: >>> >>> qqnorm(fit, form=~residuals(., type="n"), abline=c(0,1)) >>> >>> See page 239 in Pinheiro and Bates (2000) Mixed-effects models in S >>> and S-PLUS. >>> >>> Cheers, >>> >>> Simon. >>> >>> >>> On 18/06/15 03:09, Liam J. Revell wrote: >>> >>> Hi Sérgio. >>> >>> It might be worth pointing out that we do not expect that the >>> residuals from a phylogenetic regression to be normal. I >>> described this with respect to the phylogenetic ANOVA on my blog >>> ( >>> http://blog.phytools.org/2013/02/a-comment-on-distribution-of-residuals.html >>> ), >>> but this applies equally to phylogenetic regression. >>> >>> All the best, Liam >>> >>> Liam J. Revell, Assistant Professor of Biology >>> University of Massachusetts Boston >>> web: http://faculty.umb.edu/liam.revell/ >>> email: liam.rev...@umb.edu <mailto:liam.rev...@umb.edu> >>> blog: http://blog.phytools.org >>> >>> On 6/17/2015 12:40 PM, Sergio Ferreira Cardoso wrote: >>> >>> Hello all, >>> >>> I'm having a problem with a Multiple Regression PGLS >>> analysis that I'm >>> performing. The residuals are not normal and it's difficult >>> to bring them >>> to normality. In these cases, are there any alternatives to >>> the linear >>> model? I know that for non-phylogenetic analyses other >>> models exist, but is >>> there any alternative method for phylogenetic analysis? >>> Thanks in advance. >>> >>> Best regards, >>> Sérgio. >>> >>> >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> <mailto: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/ >>> >>> >>> -- >>> Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. >>> Senior Lecturer and Consultant Statistician >>> School of Biological Sciences >>> The University of Queensland >>> St. Lucia Queensland 4072 >>> Australia >>> T: +61 7 3365 2506 <tel:%2B61%207%203365%202506> >>> email: S.Blomberg1_at_uq.edu.au <http://S.Blomberg1_at_uq.edu.au> >>> http://www.evolutionarystatistics.org >>> >>> Policies: >>> 1. I will NOT analyse your data for you. >>> 2. Your deadline is your problem. >>> >>> Basically, I'm not interested in doing research >>> and I never have been. I'm interested in >>> understanding, which is quite a different thing. >>> - David Blackwell >>> >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> <mailto: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/ >>> >>> >>> >>> >>> -- >>> Com os melhores cumprimentos, >>> Sérgio Ferreira Cardoso. >>> >>> -------------------- >>> >>> Best regards, >>> Sérgio Ferreira Cardoso >>> >>> >>> >>> >>> MSc. Paleontology candidate >>> Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa >>> Geociências - Universidade de Évora >>> >>> Lisboa, Portugal >>> >> > > > -- > Com os melhores cumprimentos, > Sérgio Ferreira Cardoso. > > -------------------- > > Best regards, > Sérgio Ferreira Cardoso > > > > > MSc. Paleontology candidate > Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa > Geociências - Universidade de Évora > > Lisboa, Portugal > > [[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/ _______________________________________________ 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/
