[R-sig-phylo] Pagel 94 Baysian Version 3 states?

Hi everybody, does anyone know if the bayesian version of Pagels 94 Method of correlated binary traits is implemented in R somewhere? There is the corHMM package which implements a 3-state ML version of it, but I couldn’t find a Baysian version anywhere. So I search for a Bayesian version of a

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

Hi Manabu, thanks for that! I can see the discrete model allows 2 binaries. There is no implementation of a 3 binaries model as a pendant to corDISC, I guess?! Cheers, Franz > Am 14.06.2016 um 11:17 schrieb Manabu Sakamoto : > > Hi Franz, > > It is implemented in

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

Hi Franz, It is implemented in BayesTraits ( http://www.evolution.rdg.ac.uk/BayesTraits.html). I know it's not R, and it's a command line based program, so might take a while to get used to, but BayesTraits is really powerful (and it's Bayesian!) thanks, Manabu On 14 June 2016 at 09:58, mailbox

Re: [R-sig-phylo] Error in plotBS when number of taxa is small

HI Kamilla, can you send me your code and data and what phangorn version are you using? Cheers, Klaus On Tue, Jun 14, 2016 at 6:42 PM, Kamila Naxerova wrote: > Hi all, > > I am trying to attach bootstrap values to a small tree (just 4 taxa). > plotBS() in the phangorn

[R-sig-phylo] Error in plotBS when number of taxa is small

Hi all, I am trying to attach bootstrap values to a small tree (just 4 taxa). plotBS() in the phangorn package gives me the following error: tree <- plotBS(phylotree,bstrees,type="phylogram",p=90) Error in if (drop[j]) next : missing value where TRUE/FALSE needed This error disappears and