Hi Andrew, Simone, et al., It's probably worth adding the very minor distinction that the results of Andrew's suggested test and of phytools' phylosig test have slightly different interpretations. Assuming lambda < 1, a significant LRT when comparing the fit of a lambda model to a non-lambda, BM model using geiger would indicate that phylogenetic signal in the trait data is significantly LOWER than expected given the untransformed tree (lambda = 1). But a significant LRT from phylosig's lambda test tells you that there is significantly MORE phylogenetic signal than expected under a model where lambda = 0 (or a star phylogeny).
Perhaps that is obvious, but just in case... Best, Graham --------------------------------------------------------------------------- ------ Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 (202) 633-1316 slat...@si.edu <https://legacy.si.edu/owa/redir.aspx?C=HcyfurW5xkyXw2bWu-Td5xmRPtn7-c9I1lX iVWbeJqzfhgybLjvFBckclIN237FXoGKsGXlPAGg.&URL=mailto%3aSlaterG%40si.edu> www.fourdimensionalbiology.com <https://legacy.si.edu/owa/redir.aspx?C=HcyfurW5xkyXw2bWu-Td5xmRPtn7-c9I1lX iVWbeJqzfhgybLjvFBckclIN237FXoGKsGXlPAGg.&URL=http%3a%2f%2fwww.eeb.ucla.edu %2fgslater> On 10/11/13 1:43 PM, "Andrew Hipp" <ah...@mortonarb.org> wrote: >Dear Simone, > >You could do a likelihood ratio test on the lambda-fitted model vs. the >no-lambda model. You could also use the AICc values returned for each >model by geiger and calculate AICc weights. Brian O'Meara has a nice >summary of this on his website: > >http://www.brianomeara.info/tutorials/aic > >Take care, >Andrew > > On 10/11/2013 12:19 PM, Simone Ruzza wrote: >> Dear list, >> >> I was wondering whether you could tell me is there a way of obtaining >> a p-value for the significance of lambda when fitting a model using >> the fitContinuous, just in the same way the other function do this >> (e.g. phylosig from phytools). Apologies for the simplicity of my >> question, but I am a total beginner in phylogenetic and comparative >> methods. >> >> thanks in advance, >> >> Simone >> >> _______________________________________________ >> 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/ > > >-- >Andrew Hipp, PhD >Senior Scientist in Plant Systematics >and Herbarium Curator >The Morton Arboretum >4100 Illinois Route 53, Lisle IL 60532-1293, USA >+1 630 725 2094 >http://systematics.mortonarb.org/lab >http://quercus.mortonarb.org > >Lecturer, Committee on Evolutionary Biology >University of Chicago >http://evbio.uchicago.edu/ > >_______________________________________________ >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/
