Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Hi list, Thanks all for the help and suggestions, think I've fixed the issue! Traced the behavior can to the locale used by R. You can replicate the error by using Sys.setlocale(locale="en_US.UTF-8") and fix the issue using Sys.setlocale(locale="C") It's not clear why having certain locales as

Re: [R-sig-phylo] fitContinuous in geiger

Hi Annemarie, Positive log-likelihoods are not a problem. The log-likelihood is calculated by summing the log probability densities, which come from a function that integrates to 1.0. Thus, if the variance of this distribution is small, the value of the function will be large (i.e., greater

[R-sig-phylo] question about phyml

Hi, I have a question for phyml. When I run phymltest under R, it returned in R as a vector with the log-likelihood value of each model. I am wondering if I can obtain rate(transition/transversion ratio) matrix using R too ? I know that I can have the *.txt_phyml_stats output file after I do p

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

As a general approach, when this sort of thing happens, I'll modify and load a copy of the function that has been changed to produce a lot of debugging info (lots of dput and print statements, for example). Then what happens at each simulation step to identify where the problem occurs. [Better deve

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Hi Tanja,list Yes, everything is going extinct, but as you say, that shouldn't happen when mu = 0. > sim.bd.age(age=2,numbsim=3,lambda=2,mu=0,frac,mrca=FALSE,complete=FALSE) [[1]] [1] 0 [[2]] [1] 0 [[3]] [1] 0 > It's a rather malicious error in that, as you point out, it's a possible outcome wh

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Hi Carl, the TreeSim return (arrays of 0s) could be because TreeSim returns 0 when the tree goes extinct: treearray Array of numbsim trees with the time since origin / most recent common ancestor being age. If tree goes extinct (only possible when mrca = FALSE), returns 0. If only one e

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

drop.fossil drops all tips as well. > drop.fossil(p2) Phylogenetic tree with 0 tips and 35 internal nodes. > drop.fossil(p2, tol=.01) Phylogenetic tree with 0 tips and 35 internal nodes. not sure why it still has internal nodes (note also that trying to plot the result hangs).I've tried co

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Hi Carl & Matt, ape has drop.fossil() with a tol option set to 1e-8 by default. I wonder whether it gives different outputs than geiger's function. Best, Emmanuel -Original Message- From: Carl Boettiger Sender: r-sig-phylo-boun...@r-project.org Date: Wed, 18 May 2011 09:08:23 To: Matt

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Hi Matt, all, The other machine is also linux, but 64 bit. I've also tested it on a third linux machine, which is running R-2.10 instead of R2.13, (but is 64 bit), and it works fine there too. Only on my 32 bit linux have I observed the error. I don't seem to have another 32 bit machine lying

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

Carl, was the other machine this was working on a Linux box? I just ran into this exact problem two days ago, and it seems to have something to do with the tolerance level in Linux, as it came up in a course and I was surrounded by non-Linux computers that seemed to have no problem with the sa

[R-sig-phylo] Unexpected behavior in birth death simulations

Hi List, On one of my computers I get anomalous results from various birth-death simulations, which behave fine on my other machine. I'm quite puzzled. For instance, running the example code in geiger's birthdeath.tree and then pruning extinct taxa drops all the taxa every time, (does not happen