lme4 and sample size
On Wed, Jan 25, 2012 at 5:02 AM, Bouwmeester, W.
<W.Bouwmeester at umcutrecht.nl> wrote:
Dear professor Bates,
Is it possible to put the iteration information in an R object (this is printed when verbose=TRUE in the lmer function)?
I like to monitor this output during simulations.
About the only way to do that is to use capture.output(). The information on iterations comes from the optimizer, not from lmer.
________________________________________ Van: dmbates at gmail.com [dmbates at gmail.com] namens Douglas Bates [bates at stat.wisc.edu] Verzonden: vrijdag 13 januari 2012 17:05 To: Bouwmeester, W. Cc: R-mixed models mailing list Onderwerp: Re: lme4 and sample size On Fri, Jan 13, 2012 at 9:58 AM, Bouwmeester, W. <W.Bouwmeester at umcutrecht.nl> wrote: Dear professor Bates, I'am using the lmer function indeed. Can I use 'cvg' from the output attr(model, "dims") to evaluate convergence? (here, the object "model" is fitted with the lmer function) Yes, but do bear in mind that the cvg indicator is from the optimizer, which is nlminb in the case of the released lme4. ?We have encountered difficulties with nlminb failing to converge or giving the false convergence message or getting stuck at boundary values. ?We later switched to the bobyqa optimizer from the minqa package and then to a local implementation of the Nelder-Mead simplex optimizer. Failure to converge is a property of the optimizer being used, not the overall design of lme4. ?It happens that good optimizers that are available to Open Source projects are difficult to come by. Van: dmbates at gmail.com [dmbates at gmail.com] namens Douglas Bates [bates at stat.wisc.edu] Verzonden: vrijdag 13 januari 2012 16:51 To: Bouwmeester, W. Onderwerp: Re: lme4 and sample size I have taken the liberty of copying the reply to the R-SIG-Mixed-Models at R-Project.org mailing list so that it will be available in a searchable archive. On Fri, Jan 13, 2012 at 9:37 AM, Bouwmeester, W. <W.Bouwmeester at umcutrecht.nl> wrote: Dear professor Bates, I will incvestigate the required sample size to develop a prediction model in hierarchical data, using a simulation study. One of the model evaluation criteria will be whether the model converged. R will give warning messages if no or singular convergence appeared. Is it possible to evaluate model convergence from the cvg column in attr(mix.model,"dims")? Has this "cvg" anything to do with convergence? I saw this "cvg" output from attr(mix.model, "dims") in your publication on October 4, 2011, Linear mixed model implementation in lme4, page 6 and 20. I would strongly recommend using lmer instead of lme to fit heirarchical linear models in a simulation study. ?The lmer function in the lme4 package is much faster and more reliable than the lme function from the nlme package. The current version of lme4 on CRAN can sometimes encounter a warning about "false convergence". ?The version named lme4Eigen on the R-forge site is, in our preliminary tests, more reliable and usually faster than the released version. ?You do need to be able to build an R package from source to be able to use the lme4Eigen at present. ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.