mcmcsamp in lme4

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I fitted a mixed-effects model with a Variance Structure in nlme
(because Variance Structures are not yet implemented in lme4). After
several model fittings (with method="ML"), I found the optimal fixed
structure of my explanatory variables.

I understood from this mailing list that the p-values of the fixed
effects, given by summary(namemodel) are not trustable and thus I want
to use a Monte Carlo simulation in order to estimate the significance of
the fixed terms. This command doesn't exist in nlme, and I can't fit my
model in lme4. Is there a way to overcome this problem? Or another
function in nlme that gives comparable results?
Try intervals(fit) in 'nlme'.

================================================================
Robert A. LaBudde, PhD, PAS, Dpl. ACAFS  e-mail: ral at lcfltd.com
Least Cost Formulations, Ltd.            URL: http://lcfltd.com/
824 Timberlake Drive                     Tel: 757-467-0954
Virginia Beach, VA 23464-3239            Fax: 757-467-2947

"Vere scire est per causas scire"
There is indeed a simulate.lme() function in nlme:
can you use this to construct a Monte Carlo simulation?
i.e. (pseudocode)

 fit full model (model1)
 fit appropriate reduced model (model0)

 N times (using replicate() or a for loop) {
     simulate from reduced model, using simulate.lme(model0);
         pack it back into a copy of the original data frame
     fit full model [in lme4 there is a "refit" method that is
        more efficient, but apparently not in nlme]
            to simulated (null data)
     fit reduced model (minus one or more fixed terms), ditto
     compute/save deviance difference between full and reduced model
       as results[i]
}

compare observed deviance difference to simulated distribution:

 mean(c(results,obsdev)>=obsdev)

  cheers
    Ben
I fitted a mixed-effects model with a Variance Structure in nlme
(because Variance Structures are not yet implemented in lme4). After
several model fittings (with method="ML"), I found the optimal fixed
structure of my explanatory variables. 

I understood from this mailing list that the p-values of the fixed
effects, given by summary(namemodel) are not trustable and thus I want
to use a Monte Carlo simulation in order to estimate the significance of
the fixed terms. This command doesn't exist in nlme, and I can't fit my
model in lme4. Is there a way to overcome this problem? Or another
function in nlme that gives comparable results?

Thanks a lot,

Sebastiaan

Sebastiaan De Smedt

Research assistant

UA - Department of Bioscience Engineering

Groenenborgerlaan 171 - V6.16

B-2020 Antwerpen, Belgium

+32 (0)3 265 34 51

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Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
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