alanc at umit.maine.edu
Mon Mar 31 00:48:08 CEST 2008
I hope I didn't offend. I guess I was hoping that there was a reason to neglect autocorrelation, transform it away, or "trick" lme4 into handling it. I couldn't see a solution in any of those three categories, but I figured that posting the query
was the way to find out if I missed something.
I do infer from your response that there is no obvious way to "trick" lme4 into handling autocorrelated error terms without modifying the source. But I'd be happy for someone to demonstrate that I'm incorrect (for some value of "obvious").
Even though the lme4 software is excellent regardless of the funding source, I do appreciate that you shared the background regarding the funding, as puts the design decisions into a very helpful perspective. You didn't have to justify your design
decisions, but I'm glad you did. Thank you.
I'm looking forward to the book. Everyone on this list knows that nlme + Pinheiro & Bates were excellent contributions, and I'm sure that lme4 + the book on multilevel modeling in R will be as well.
"Douglas Bates" <bates at stat.wisc.edu> on Sunday, March 30, 2008 at 5:43 PM -0500 wrote:
>On Sat, Mar 29, 2008 at 2:52 PM, Alan Cobo-Lewis <alanc at umit.maine.edu> wrote:
>> Doug Bates writes on r-sig-mixed-models at r-project.org on Saturday, March 29, 2008 at 7:00 AM -0500 wrote about his planned book on multilevel modelling in R:
>> >I emphasize graphical displays of the data and aspects
>> >of the fitted models and inferences based on MCMC samples from the
>> >posterior distribution of the model parameters.
>> (n)lme handled correlated error terms, but lme4 does not.
>So if you want a model with correlated error terms (in addition to the
>correlation induced by the random effects) then you should use the
>> Leaving aside the superior algorithms in lme4, this appears to be the major impediment to considering lme4 capabilities as a superset of (n)lme capabilities.
>I don't recall any statements to the effect that the lme4 capabilities
>would be a superset of the nlme capabilities. It seems that whoever
>made that decision should have informed me of it.
>The development of the lme4 package has been generously funded by
>several grants, the most important of which was an STTR contract that
>we had for 3 years. The purpose of that contract was to develop a
>package that could fit generalized linear mixed models using the
>Laplace approximation and allowing for crossed or partially crossed
>grouping factors for the random effects. The development is currently
>funded by another grant specifically to provide for fitting models
>with crossed and partially crossed random effects and with carryover
>of random effects from one time period to another.
>Neither generalized linear mixed models nor models with crossed or
>partially crossed random effects can be fit (well without resorting to
>egregious kludges) with the nlme package. Even nonlinear mixed models
>as fit by nlme are sub-optimal compared to the methods in lme4. (lme4
>uses direct optimization of the Laplace approximation to the
>log-likelihood whereas nlme uses an alternating algorithm that Mary
>Lindstrom and I proposed.)
>My priorities are to fulfill the tasks that I proposed for these
>grants and to build the best software that I can. The beauty of open
>source software is that if your priorities are different, you have
>full access to the sources and you can modify them to fulfill your
>objectives. So I suggest that you
> - Continue to use the nlme package if you wish to incorporate
>(additional) correlation structures in models
> - Design, code, test and document extensions to the lme4 package to
>do so and then submit these changes as patches
> - Develop your own package so you can have things done the way you
>want them to be done. You already have access to the lme4 sources so
>a lot of the heavy lifting has been done for you.
>This developing the software is not as easy as it may seem. There are
>many trade-offs and, at least for me, it takes a lot of effort to
>determine even if it is possible to incorporate various extensions
>harmoniously. It is possible to model the mean and variance of the
>conditional distribution of the response separately when that
>distribution is multivariate normal. It is not as easy to do so when
>that distribution is binomial or Poisson or some other distribution
>for a generalized linear mixed model. Because the first purpose of
>the lme4 package was to allow for generalized linear mixed models I
>did not incorporate (additional) correlation structures and variance
>functions. I'm not even sure it could be done consistently for GLMMs
>but you are welcome to show us how.
>> But what do I do if I've got, for example, autocorrelated error terms? Is there a way to "trick" lme4 into handling that (perhaps something analogous to the "random effect variance per treatment group in lmer" thread that David Afshartous and I
>> participated in)? Is there instead a good argument for ignoring it? It seems like something that would arise in practice in a non-negligible amount of problems in real data. Will the upcoming book give some advice on how to address this?
>> I can produce self-contained reproducible code if necessary, but I don't think it is.
>> R-sig-mixed-models at r-project.org mailing list
Alan B. Cobo-Lewis, Ph.D. (207) 581-3840 tel
Department of Psychology (207) 581-6128 fax
University of Maine
Orono, ME 04469-5742 alanc at maine.edu
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