Hi Manabu, yes it's true. In fact it depends what you are looking for. It was mainly for warning people trying to size-standardize their data because some expect then to work without size related differences.Using the residuals is somewhat a different approach cheers, Julien > Date: Fri, 19 Jun 2015 15:19:59 +0100 > From: manabu.sakam...@gmail.com > To: sclaramunt...@gmail.com > CC: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Non Parametric PGLS > > Mosimann's method should remove isometric scaling, so the resulting values > will retain allometric information. I guess if you regard allometric shape > difference as an undesired feature of your data, then you can call it > biased. But if you wan to investigate allometry without the effect of size, > then that's really what you want, isn't it? > cheers, > Manabu > > On 19 June 2015 at 14:57, Santiago Claramunt <sclaramunt...@gmail.com> > wrote: > > > 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/ > > > > > > -- > Manabu Sakamoto, PhD > manabu.sakam...@gmail.com > > [[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]]
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