Re: [R-sig-phylo] estimate likelihood of data for given model and parameters

Hi Carl (also Brian), This can effectively be accomplished in the geiger function fitContinuous() by setting the upper & lower bounds for the parameter to both be equal to the value for which you want to calculate the likelihood. Unfortunately, these are not allowed to be exactly the same; h

Re: [R-sig-phylo] estimate likelihood of data for given model and parameters

I have code for this in my TreEvo package (on R-forge -- see brownieneglnL in ) though note that the package itself is not all cleaned up into install.packages()-ready form. You could also

[R-sig-phylo] estimate likelihood of data for given model and parameters

Dear r-sig-phylo, I'd like to be able to estimate the likelihood of a model with a given Brownian rate parameter under a given data set. For OU models, this can be accomplished through the ouch package with the flag fit=FALSE. However there does not seem to be a corresponding option for Brownian

Re: [R-sig-phylo] plot.phylo leftwards in ape

Hi Brian, It's fixed and in the SVN: https://svn.mpl.ird.fr/ape/dev/ape/R/plot.phylo.R Due to some coding complications, you'll certainly need to use 2 values for x.lim, eg: plot.phylo(bird.orders, direction="l", x.lim=c(-15, 38)) Cheers, Emmanuel Brian O'Meara a écrit : I'm trying t

Re: [R-sig-phylo] apTreeshape

Dear all, The package apTreeshape is back on CRAN (http://cran.r-project.org/web/packages/apTreeshape/index.html). I hope that this short interruption did not cause you too much trouble. Sincerely, Michael Blum -- -- Michael BLUM Chargé de recherche (CR2 CNRS) (Research A