[R-sig-ME] Bootstrapping an lmer model

[Douglas Bates]

On Thu, Nov 3, 2011 at 2:44 PM, Hugo Mildenberger
<Hugo.Mildenberger at web.de> wrote:
> Christoph,
>
>
> it appears as if lme4 had dropped the $ operator. A first step to cope
> with that is to replace "object$call" with "object at call" in
> "Zelig/R/bootfn.default.R" (i.e. in Zelig package sources),

I don't think that fm$call ever worked with lme4.  The '4' in the name
is from the use of S4 classes so the only thing that would have worked
is fm at call.

As of R-2.14.0 there is a base-R function called getCall() which is
now used in update, exactly to hide these discrepancies between fitted
models represented at S3 or S4 objects.  So the preferred form is
getCall(fm) instead of either fm$call or fm at call

> another
> involves editing "param.mixed.R" at the same place. But that still isn't
> enough, because then boot::boot runs into an array index error. I'm
> attaching a patch against the source tree contained in
> Zelig_3.5.1.tar.gz, but I almost sure that the param.mixed.R patch is
> not the right solution, whereas the patch against bootfn.default.R may
> interfere with other packages. I'd contact the package's authors at this
> point. The remaining
>
>  Error in t.star[r, ] <- res[[r]] :
>    incorrect number of subscripts on matrix
>
> stems from boot::boot:
>
>  120     t.star <- matrix(, RR, length(t0))
>  121     for (r in seq_len(RR)) t.star[r, ] <- res[[r]]
>
> res[[r]] is the list returned by param.mer() as defined in
> Zelig/R/param.mixed.R  I'd think it can't be correct to assign a nested
> list to  t.star. t.star is a matrix with dimensions 100, 3.
>
>
> I hope this still helps a bit.
>
>
> Best regards,
>
> Hugo
>
>
>
> Am 03.11.2011 14:55, schrieb Christoph Scherber:
>> Dear all,
>>
>> Has anyone written some code to get predicted values from an lmer model using bootstrapping?
>>
>> The only available method seems to be the sim() function in package "Zelig". This works well if you don愒 do bootstrapping. However, it doesn愒 seem
>> to work for bootstrap=TRUE:
>>
>> ##
>> require(Zelig)
>> data(voteincome)
>>
>> z.out1 <- zelig(vote ~ education + age + female + tag(1 | state),
>> data = voteincome, model = "logit.mixed")
>>
>> x <- setx(z.out1, education = 4)
>> s.out1 <- sim(z.out1, x = x, bootstrap=TRUE)
>>
>> #Error in `*tmp*`$call : $ operator not defined for this S4 class
>>
>> ##
>>
>> I扉e tried to modify some of the internal code from the sim() function, but couldn愒 get it to work until now.
>>
>> I would greatly appreciate any help, ideas or suggestions.
>>
>> Best wishes,
>> Christoph
>>
>> (using R 2.13.2 on Windows 7 64-Bit)
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
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