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: [email protected] > Date: Fri, 19 Jun 2015 08:57:11 -0500 > To: [email protected] > 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 <[email protected]> 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: [email protected] > > > Date: Thu, 18 Jun 2015 12:52:11 -0500 > > > To: [email protected] > > > 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 > > > <[email protected]> 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 <[email protected]>: > > > > > > > >> 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: [email protected] > > > >> 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 <[email protected] > > > >>> <mailto:[email protected]>>: > > > >>> > > > >>> > > > >>> 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: [email protected] <mailto:[email protected]> > > > >>> 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 - [email protected] > > > >>> <mailto:[email protected]> > > > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > >>> Searchable archive at > > > >>> http://www.mail-archive.com/[email protected]/ > > > >>> > > > >>> > > > >>> -- > > > >>> 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 - [email protected] > > > >>> <mailto:[email protected]> > > > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > >>> Searchable archive at > > > >>> http://www.mail-archive.com/[email protected]/ > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> -- > > > >>> 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 - [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]/ > > > [[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]/ [[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]/
