Dear all, Following up this conversation; Using OUwie, i get reasonable values for theta under several models for all my traits, but one. In this case, this is a trait which can only take positive values and i get negative theta values for all the different models, including BM and OU1. the standard error is not big enough to consider my theta value to be around zero. (for example: theta = -2.279, se= 0.209). Any idea of what could be causing this and if it is possible to force OUwie to estimate theta within certain boundaries?
Thank you, Sandra. 2013/10/29 Marguerite Butler <mbutler...@gmail.com> > Hi Sandra and others, > > You can also assess confidence using parametric bootstrap, a procedure > which we generally recommend for all users. ouch has built-in facilities to > do so (the bootstrap() and simulate() functions in addition to update() ). > I think there are examples in my tutorial. If not, let me know and I can > send you another. > > Marguerite > > On Oct 29, 2013, at 6:08 AM, Cecile Ane <a...@stat.wisc.edu> wrote: > > > FYI, we have some theory to explain why alpha has large standard errors > and in which conditions. As Brian says, it comes with a flat likelihood > with respect with alpha. > > http://dx.doi.org/10.1214/13-AOS1105 or > http://www.stat.wisc.edu/~ane/publis/2013HoAne_AoS.pdf > > > > On 10/29/2013 09:46 AM, Brian O'Meara wrote: > >> In at least the OUwie paper we spent a lot of time doing simulations to > >> determine this empirically (this may have been examined in other papers, > >> too, though none come to mind). Alpha can be estimated, but sometimes > with > >> scarily large standard errors (but not always). This property should > hold > >> for related methods (it's a property of the likelihood surface for these > >> models). You can just plot the alpha values vs likelihood to get a > sense of > >> this surface for your dataset (ideally, estimating the other parameters > for > >> each fixed alpha, which is possible, though the kludge of holding the > other > >> parameters at their MLE and just varying alpha will give you a sense of > the > >> surface, though it's a bit non-conservative). We had code in OUwie to > do a > >> contour plot of the likelihood surface but took it out (a small > licensing > >> difference between akima (university license) and OUwie (GPL) led to > OUwie > >> being pulled from CRAN by the CRAN maintainers until we resolved the > >> difference). > >> > >> Brian > >> > >> > >> _______________________________________ > >> Brian O'Meara > >> Assistant Professor > >> Dept. of Ecology & Evolutionary Biology > >> U. of Tennessee, Knoxville > >> http://www.brianomeara.info > >> > >> Students wanted: Applications due Dec. 15, annually > >> Postdoc collaborators wanted: Check NIMBioS' website > >> Calendar: http://www.brianomeara.info/calendars/omeara > >> > >> > >> On Tue, Oct 29, 2013 at 10:21 AM, sandra goutte <gou...@mnhn.fr> wrote: > >> > >>> Thank you Marguerite. Looking at OUwie and OUCH/SLOUCH, i see that > alpha is > >>> estimated along the other parameters, whereas in Hansen 1997 and other > >>> papers it is suggested that this would lead to very large standard > errors. > >>> Is that problem resolved in these functions? > >>> > >>> Best, > >>> Sandra. > >>> > >>> > >>> 2013/10/26 Marguerite Butler <mbutler...@gmail.com> > >>> > >>>> Dear Sandra, > >>>> > >>>> You might also want to look at the papers that go along with slouch, > >>> ouch, > >>>> and ouwie. Here are some pdfs, along with some tutorials. > >>>> > >>>> On my Rcompstart, the ouch stuff starts around page 165 > >>>> > >>>> Let me know if you need help with ouch. > >>>> > >>>> Marguerite > >>>> > >>>> > >>>> > >>>> On Oct 24, 2013, at 7:03 AM, sandra goutte <gou...@mnhn.fr> wrote: > >>>> > >>>> Dear list, > >>>> > >>>> My aim is to compare the fit of models for which *theta* is allowed to > >>>> change at different nodes (different combinations of 1 ,2 or 3 > nodes). I > >>>> don't really understand the calculation of the deviance, but if i'm > not > >>>> mistaken the difference between the deviances of 2 models follows a > >>>> *chi*square distribution with the difference of parameters in the > >>>> models as > >>>> degree of freedom. Now, how to compare two models with the same > number of > >>>> optimum changes but at different nodes? > >>>> > >>>> I am having a hard time understanding the details of the function with > >>>> regards to Hansen's (1997) paper. What is the relationship between the > >>>> deviance and the RSS from Hansen (1997)? Is it possible to calculate > the > >>>> RSS from the output of compar.ou ? > >>>> > >>>> I would appreciate any advice or insight on the subject! > >>>> Sandra. > >>>> > >>>> -- > >>>> PhD Student > >>>> Muséum National d'Histoire Naturelle > >>>> Département Systématique et Évolution > >>>> USM 601 / UMR 7205 Origine, Structure et Évolution de la Biodiversité > >>>> Reptiles & Amphibiens - Case Postale 30 > >>>> 25 rue Cuvier > >>>> F-75005 Paris > >>>> > >>>> Tel : +33 (0) 1 40 79 34 90 > >>>> Mobile: +33 (0) 6 79 20 29 99 > >>>> > >>>> [[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/ > >>>> > >>>> > >>>> ____________________________________________ > >>>> Marguerite A. Butler > >>>> Associate Professor > >>>> > >>>> Department of Biology > >>>> University of Hawaii > >>>> 2538 McCarthy Mall, Edmondson Hall 216 > >>>> Honolulu HI 96822 > >>>> > >>>> Office: 808-956-4713 > >>>> Dept: 808-956-8617 > >>>> Lab: 808-956-5867 > >>>> FAX: 808-956-9812 > >>>> http://www.hawaii.edu/zoology/faculty/butler.html > >>>> http://www2.hawaii.edu/~mbutler > >>>> http://www.hawaii.edu/zoology/ > >>>> > > > > -- > > Cecile Ane > > Departments of Statistics and of Botany > > University of Wisconsin - Madison > > www.stat.wisc.edu/~ane/ > > > > CALS statistical consulting lab: > > www.cals.wisc.edu/calslab/stat_consulting.php > > > > _______________________________________________ > > 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/ > -- PhD Student Muséum National d'Histoire Naturelle Département Systématique et Évolution USM 601 / UMR 7205 Origine, Structure et Évolution de la Biodiversité Reptiles & Amphibiens - Case Postale 30 25 rue Cuvier F-75005 Paris Tel : +33 (0) 1 40 79 34 90 Mobile: +33 (0) 6 79 20 29 99 [[alternative HTML version deleted]]
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