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/ > > > > > > > > > > > > > > > > > > > > > > > -- > 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/ > [[alternative HTML version deleted]]
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