I think Etienne makes it definitely clearer. It's was not to prevent the use of Mosimann method, but to say that it has a different goal than the regression (or even better the ANCOVA) approach.Thus, it's worth considering the points highlighted by Liam in his paper.
All the best, Julien > From: sclaramunt...@gmail.com > Date: Fri, 19 Jun 2015 10:46:01 -0500 > To: eleve...@uottawa.ca > CC: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Non Parametric PGLS > > Thanks Manabu and Etienne for the clarifications; that was also my > understanding of Mosimann’s method. > I like Mosimann’s approach because it has two fundamental properties: > > 1) it is grounded in a basic geometric definition of shape and size: two > objects have the same shape if they have the same proportions in all > dimensions. (this may not be the case using the PCA or residuals approaches, > in which objects of exactly the same shape can have different PCA scores or > residuals if they are of different size). > > 2) the size and shape of an object do not depend on other objects/species in > the sample and therefore do not need consideration of the phylogeny in > interspecific data (size and shape in PCA and regression approaches depend > on the characteristics of the entire sample of objects/species and therefore > require consideration of phylogeny) > > Julien: It seems that some of the axes of your plots are mislabeled. > > > Santiago > > On Jun 19, 2015, at 9:47 AM, Étienne Léveillé-Bourret <eleve...@uottawa.ca> > wrote: > > > Hello Santiago, > > > > > > I think that what Julien means is that under pure isometry, Mosimann's > > method gives the same result as taking the residuals of a linear > > regression. This doesn't mean that Mosimann's method is not good for > > allometric cases, it means that it gives a different result compared to the > > residuals method, which is expected since it is not the same method. > > > > If what you want is to preserve shape information, then Mosimann's method > > is the best (only?) way to go. Taking residuals will remove shape > > information when shape is correlated with size, as in allometry. There is > > no bias in the fact that shape resulting from Mosimann ratios is correlated > > with size; this is the very definition of allometry. See Jungers et al. > > (1995). > > > > So you need to ask yourself: do you want to standardize individuals and > > preserve all shape information (Mosimann methods) or do you want to > > standardize individuals to preserve only shape information that is > > uncorrelated with size (residuals methods)? > > > > > > Cheers, > > Étienne L.-B. > > > > ref.: > > Jungers WL, Falsetti AB, Wall CE. 1995. Shape, relative size, and > > size‐adjustments in morphometrics. American Journal of Physical > > Anthropology 38: 137–161. > > > > > > > From: sclaramunt...@gmail.com > > > Date: Fri, 19 Jun 2015 08:57:11 -0500 > > > To: r-sig-phylo@r-project.org > > > Subject: Re: [R-sig-phylo] Non Parametric PGLS > > > > > > Hi Julien, > > > > > > Mosimann’s method was proposed for the study of allometry, so it would be > > > strange if it only applies to isometric cases. Can you provide further > > > details or suggest readings? > > > > > > Cheers, > > > > > > Santiago > > > > > > On Jun 18, 2015, at 7:06 PM, Julien Clavel <julien.cla...@hotmail.fr> > > > wrote: > > > > > > > Hi Sergio, > > > > > > > > Just to precise that you have to keep in mind that Mosimann ratio (if > > > > you are speaking about the Mosimann shape ratio, e.g. with the > > > > geometric mean) applies only when there is an isometric relationship > > > > (as for most analysis based on ratio). You should check first, > > > > otherwise the resulting standardized values will be biased. Although > > > > the residuals solution is probably not the best, there is no magic > > > > solution to size standardization... > > > > By the way remember that on log spaces isometry is represented by a > > > > slope of 1, and on arithmetic scales by an intercept of zero. The > > > > resulting bias in the ratio are thus different. > > > > > > > > Best, > > > > > > > > Julien > > > > > > > > > From: sclaramunt...@gmail.com > > > > > Date: Thu, 18 Jun 2015 12:52:11 -0500 > > > > > To: r-sig-phylo@r-project.org > > > > > Subject: Re: [R-sig-phylo] Non Parametric PGLS > > > > > > > > > > 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/ > > > > > > > > > [[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/ > > > [[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/ [[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/
