Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Thank you all for these nice and very very helpful answers... it seems that I have some work to do for a little while now. I'll give a try to all the hints and pieces of code you sent me, and may get back to you off-list for feedbacks or more precise requests. Thanks again Seb Le 04/08/2010 21:

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Hi all. Here is some code that I think will do what Dr. Felsenstein has suggested for a single character. It returns a vector containing the simulated states at all internal or terminal nodes, numbered according to the numbers used in tree$edge. Happy to hear if this works. See below: # c

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Luke wrote: > The simulations in Geiger do draw from a mvn distribution but - in an > unnecessary step - draw random numbers for every branch and use matrix > multiplication to get the tip values. This is kind of dumb and needlessly > slow but does give you the right answer. Carl is correct t

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Jeepers it can be hard to even keep up with this mailing list sometimes - you all are great! The simulations in Geiger do draw from a mvn distribution but - in an unnecessary step - draw random numbers for every branch and use matrix multiplication to get the tip values. This is kind of dumb an

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Hi Sebastien, I believe the simulation simply draws random numbers from the appropriate multivariate normal distribution determined by the model's covariance matrix for the tip values. This means that a complete trajectory of trait values in never actually generated. This is much more efficient

Re: [R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

I forgot to mention that I am willing to do this with continuous traits. Thanks to those who already answered (about discrete characters unfortunately). Seb Le 04/08/2010 15:03, Sebastien Lavergne a écrit : Hi everybody, I have a question regarding the sim.char function in geiger. Does anybod

[R-sig-phylo] retrieving simulated ancestral states from sim.char{geiger}

Hi everybody, I have a question regarding the sim.char function in geiger. Does anybody foresee an easy way to retrieve the simulated ancestral states ? (i.e. the values of each trait for all internal nodes of the tree) Does this sound doable ? Any hint about how to do it ? Thanks for your hel