From: Jack Tanner <ihok_at_hotmail.com>

Date: Thu 05 Jan 2006 - 01:59:49 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jan 05 02:10:25 2006

Date: Thu 05 Jan 2006 - 01:59:49 EST

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 <spencer.graves@pdf.com>
**>To: Jack Tanner <ihok@hotmail.com>
**>CC: r-help@stat.math.ethz.ch, Douglas Bates <dmbates@gmail.com>,
**>Prof Brian Ripley <ripley@stats.ox.ac.uk>
**>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.
**>>
**>>______________________________________________
**>>R-help@stat.math.ethz.ch mailing list
**>>https://stat.ethz.ch/mailman/listinfo/r-help
**>>PLEASE do read the posting guide!
**>>http://www.R-project.org/posting-guide.html
*

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jan 05 02:10:25 2006

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