Thank you, Spencer. I've discovered that if I drop the value parameter from the call to corSymm(), R 2.2.1 converges successfully, but the values it converges to are slighly (in the hundredths and thousandths) different from those that R 2.1.1 produces.
In the same vein, I also have an example where the R 2.2.1 glmmPQL produces the warning "non-integer #successes in a binomial glm! in: eval(expr, envir, enclos)", and another where R 2.2.1 says "iteration limit reached without convergence" unless I invoke glmmPQL() with lmeControl(msMaxIter=100). Neither of those happen in R 2.1.1. I'm fine with the results above. I don't know if they're of interest to anyone else; if they are, I'm happy to provide more details. >From: Spencer Graves <[EMAIL PROTECTED]> >To: Jack Tanner <[EMAIL PROTECTED]> >CC: [email protected], Douglas Bates <[EMAIL PROTECTED]>, >Prof Brian Ripley <[EMAIL PROTECTED]> >Subject: Re: [R] unexpected "false convergence" >Date: Tue, 03 Jan 2006 20:40:56 -0800 > > I replicated your 'false convergence' using R 2.2.0: > > sessionInfo() >R version 2.2.0, 2005-10-06, i386-pc-mingw32 > >attached base packages: >[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" >[7] "base" > >other attached packages: > nlme MASS >"3.1-66" "7.2-23" > > Since the error message said, "Error in lme.formula", I listed the > code >for "lme.formula" and traced it using "debug(lme.formula)", The function >"glmmPQL" calls "lme.formula" repeatedly. The function "lme.formula" in >turn calls "nlminb" when it's available, though it used to call "optim". >The fifth time "lme.formula" was called, "nlminb" returned the error >message "false convergence (8)". > > Under R 2.2, "nlminb" is part of the "base" package. I'm not > certain, >but I don't think it was available in "base" under R 2.1.1. > > I think this explains the problem, but not how to fix it. I tried >modifying the code fo "lme.formula" to force it to call "optim", but this >generated a different error. I am therefore copying Professors Bates & >Ripley in case one of them might want to look at this. > > hope this helps. > spencer graves > >Jack Tanner wrote: >>I've come into some code that produces different results under R 2.1.1 and >>R 2.2.1. I'm really unfamiliar with the libraries in question (MASS and >>nlme), so I don't know if this is a bug in my code, or a regression in R. >>If it's a bug on my end, I'd appreciate any advice on potential causes and >>relevant documentation. >> >>The code: >> >>score<-c(1,8,1,3,4,4,2,5,3,6,0,3,1,5,0,5,1,11,1,2,4,5,2,4,1,6,1,2,8,16,5,16,3,15,3,12,4,9,2,4,1,8,2,6,4,11,2,9,3,17,2,6) >>id<-rep(1:13,rep(4,13)) >>test<-gl(2,1,52,labels=c("pre","post")) >>coder<-gl(2,2,52,labels=c("two","three")) >>il<-data.frame(id,score,test,coder) >>attach(il) >>cs1<-corSymm(value=c(.396,.786,.718,.639,.665,.849),form=~1|id) >>cs1<-Initialize(cs1,data=il) >>run<-glmmPQL(score~test+coder, >>random=~1|id,family=poisson,data=il,correlation=cs1) >> >>The output under R 2.2.1, which leaves the run object (last line of the >>code) undefined: >> >>iteration 1 >>iteration 2 >>iteration 3 >>iteration 4 >>Error in lme.formula(fixed = zz ~ test + coder, random = ~1 | id, data = >>list( : >> false convergence (8) >> >>Under R 2.1.1, I get exactly 4 iterations as well, but no "false >>convergence" message, and run is defined. >> >>______________________________________________ >>[email protected] mailing list >>https://stat.ethz.ch/mailman/listinfo/r-help >>PLEASE do read the posting guide! >>http://www.R-project.org/posting-guide.html ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
