Hi Nick, it's running (or trying to) on diversitree v0.9-7
Kev ________________________________ From: Nicholas Crouch [ncro...@uic.edu] Sent: 01 April 2014 17:01 To: Arbuckle, Kevin Subject: Re: [R-sig-phylo] Error in diversitree with MuSSE models Kev, What version of diversitree are you running? Nick On Apr 1, 2014 10:50 AM, "Arbuckle, Kevin" <k.arbuc...@liverpool.ac.uk<mailto:k.arbuc...@liverpool.ac.uk>> wrote: Hi, I am trying to run a set of MuSSE models in diversitree but getting error messages that I can't seem to figure out (fortunately the models are only an adjunct to my main premise, not particularly vital). The trait has 4 levels and the full model works fine, with the following code:- lik<-make.musse(contree,col,k=4,sampling.f=0.33) start<-starting.point.musse(contree,k=4) fit<-find.mle(lik,start) However, when I then try and run a fully constrained model (with only a single speciation rate, extinction rate, and transition rate) with the following code:- lik.allcon<-constrain(lik,lambda1~lambda2,lambda2~lambda3,lambda3~lambda4,mu1~mu2,mu2~mu3,mu3~mu4,q12~q13,q13~q14,q14~q21,q21~q23,q23~q24,q24~q31,q31~q32,q32~q34,q34~q41,q41~q42,q42~q43) fit.allcon<-find.mle(lik.allcon,start[-c(1,2,3,5,6,7,9,10,11,12,13,14,15,16,17,18,19)]) I get the following error message:- Error in check.pars.nonnegative(pars, k * (k + 1)) : Parameters must be non-negative and finite I don't quite understand why or how to fix this. I have previously run BiSSE models (including with constraints) on the same dataset (just with different coding of some levels which made the trait binary) and had no problems. After looking through the diversitree manual I have tried specifying/changing the fail.value and method arguments in find.mle, but I get exactly the same message. Any help or ideas would be greatly appreciated. I presume it is something introduced via the constraints since the full model runs fine, but other than that I am none the wiser. Thanks, Kev [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
