[R-sig-phylo] [function like ratebystate, but for discrete characters?]

Hello, Quick question. I'm interested in whether the presence/absence of character 'A' affects the rate of evolution in character 'B'. Is there a function that will do this for two or more discrete characters? I've seen ratebystate {phytools} for continuous data; but my data are all binary!

Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?]

Hi Michael. This is essentially the method of Pagel (1994). Though often interpreted as a test for correlated evolution of two binary characters, the model that is actually being fit is one in which the rate of transition 0->1 (or vice versa) in character A is affected by the state of binary

Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?]

Also see BayesTraits for the bayesian version. Jake > On May 3, 2016, at 8:11 PM, Liam J. Revell wrote: > > Hi Michael. > > This is essentially the method of Pagel (1994). Though often interpreted as a > test for correlated evolution of two binary characters, the model

Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?]

Hi Liam, Thank you for your quick reply! Been playing around with fitPagel{phytools} and corDISC{corHMM}. That makes sense; state-dependent model, so just look at the transition rates between characters! This might be a silly question, but I'll ask it anyways. For the traits that I'm