[R-sig-phylo] Pagel's lambda for single trait

Hi, how do i get the actual lambda value using fitDiscrete? it's for a binary trait over a phylogeney. And would i need a p value too, for loglikelihood ratio test between this lambda model and another model? thanks! >lambda<-fitDiscrete(tree,trait,treeTransform="lambda") >lambda GEIGER-fitted

Re: [R-sig-phylo] Pagel's lambda for single trait

Hi Xinxin. In the current CRAN version of geiger treeTransform is not a valid argument of fitDiscrete, instead you probably want to do: fit<-fitDiscrete(tree,trait,transform="lambda") Then the fitted value of lambda will be: fit$opt$lambda All the best, Liam Liam J. Revell, Associate

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

Hi Jacob, There is a package named OutBreakTools ( https://cran.r-project.org/web/packages/OutbreakTools/index.html) that includes a function named "read.annotated.nexus". It will retrieve all metadata from trees produced by BEAST/TreeAnnotator. I found particularly useful that you can also