Re: [R-sig-phylo] Question on pCCA (phyl.cca)

Dear Liam and Julien, Thank you both for your help. I have tried both solutions on the same dataset under a BM model to compare them. I expected to get similar results, at least for the general conclusions on the significance of correlations. for Julien's solution, I ran: model<-mvBM(tree,

Re: [R-sig-phylo] Question on pCCA (phyl.cca)

Oi Julien, Yes you are right, I was comparing things that are not the same! However, even changing the p-values as you suggested, the conclusions (which is really what i'm interested in) are still much different between the two methods. For the example I gave above, the correlation is still not

[R-sig-phylo] Question on pCCA (phyl.cca)

Dear list, I have 2 sets of continuous variables (acoustic and environmental) and a phylogeny for a group of species. I am looking for correlations between the environmental variables and the acoustic ones. I ran a pCCA (phyl.cca {phytools} ), which gave me p-values for the correlations of each

Re: [R-sig-phylo] compar.ou

://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

Re: [R-sig-phylo] compar.ou

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

Re: [R-sig-phylo] compar.ou (sandra goutte)

Thank you both for your answers, i will look into those packages. Best, Sandra. 2013/10/25 Brian O'Meara bome...@utk.edu You can also use OUwie for a variety of models (OU with different means and/or different variances and/or different attraction values), but it returns AIC and lnL scores

[R-sig-phylo] compar.ou

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

[R-sig-phylo] problem with corMartins (ape)

Dear list, I am trying to run a gls with an OU correlation structure using corMartins. I first wanted to check whether i had a phylogenetic autocorrelation in my trait, so i used the Moran's I index (Moran.I): vcovm-vcv(corMartins(1,tree, fixed=T)) Moran.I(trait, vcovm, alt=greater) And i

Re: [R-sig-phylo] compare.gee issues with multiple predictor models

Hi Emmanuel, Thank you so much for those answers! Sandra. 2013/7/3 Emmanuel Paradis emmanuel.para...@ird.fr Hi Sandra, Le 01/07/2013 22:03, sandra goutte a écrit : Hello all, I am sorry if the question has already been answered, i have not found it int the archive. I am using

[R-sig-phylo] compare.gee issues with multiple predictor models

Hello all, I am sorry if the question has already been answered, i have not found it int the archive. I am using compar.gee to look at possible correlations between behavioral traits and ecological variables. I have two problems: 1) if i try a model with more than 3 predictors, the function

Re: [R-sig-phylo] using ace (ape) with missing data

' website Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Jun 12, 2013 at 11:10 AM, sandra goutte gou...@mnhn.fr wrote: Hi Luke, Thank you for your message. I know that the Continuous section of BayesTraits accepts missing data, but i haven't found any information on how

[R-sig-phylo] using ace (ape) with missing data

Hello everyone, I am new to the r-sig-phylo mailing list; I have looked up in the archives, but i haven't found any answer to my question, so here it is: I have a tree with 156 tips, and various data sets (morphology, ecology, behavioral data; continuous and discrete), but i have missing data,