[R-sig-phylo] Problem on LAGOPUS package

Hi, I'm sending this email because I want to use PAML/multidivtime approach implemented in the R package Lagopus. I followed instructions from the manual but I have a problem with the multidivtime() function. When I execute: multidivtime(x,file=NULL,start=‘’baseml’’, part=1, runs = 4,

Re: [R-sig-phylo] getBtimes vs. branching.times

Lev, This is easy, if the newick strings are structured the same so that the resulting edge matrix and tip labels are identical. Here's a worked example: ``` library(ape) # with edge lengths

Re: [R-sig-phylo] getBtimes vs. branching.times

Dear David and Santiago, Thank you very much! Indeed, tree3$node.label<-tree2$node.label is pretty obvious once one figures out the structure of tree! -- Lev From: Santiago Sánchez > Date: Thu, 14 Jan 2016 09:48:16 -0700 To:

Re: [R-sig-phylo] getBtimes vs. branching.times

Dear Lev, I simple way to do what you request would be to follow this example with your data: > library(ape) # here I'm creating a random tree with branch lengths > treeBL <- rtree(10) > treeBL$edge.length [1] 0.59962263 0.76458987 0.48171189 0.26387301 0.76967429 0.42754456 [7] 0.30173612

Re: [R-sig-phylo] Problem on LAGOPUS package

Hi Charles I encountered the same error, and just commented out the following line in the multidivtime function: #write(paste(" kappa = ", kappa, "* initial or fixed kappa",sep = ""), filename, append = TRUE) That seemed to allow the function to proceed, but then I ran into