Does the "confint-MASS" function from the MASS library do the profile 
likelihood confidence interval you are recommending?  From the 
documentation it appears to.  I just upgraded to R version 2.12.2.  In 
the previous version of R it was just called "confint", but apparently 
it was changed to avoid confusion.

Phil Chapman
Colorado State University

On 3/24/2011 8:15 AM, Douglas Bates wrote:
> On Wed, Mar 23, 2011 at 7:31 PM, Sandra M. Durán<sduran@ualberta.ca>  wrote:
>> Hi, I want to evaluate if bird species respond strongly to management,
>> vegetation or both. I am running different models with different species.
>> Here is the overall formula here:
>> print(fm1<- glmer(birds ~ ownership + (1 | site), family=poisson,
>> data=wma))
>> And I want to know the syntax to get the confidence intervals (lower and
>> upper limit) for the parameters in the fixed effects. I have used:
>> confint(fm1), but I get an error message, although this code has worked for
>> me when I used glm. It is possible to specify the confidence level(0.90,
>> 0.95)?
> A way of getting approximate confidence intervals is to use the
> coefficients table from the summary for the model, as shown in the
> enclosed.
>
> These confidence intervals are approximations.  A more reliable
> approach would be to profile the deviance with respect to the
> parameters of interest but that has not yet been implemented.
>
> Note that in cases like this example and for your example confidence
> intervals on coefficients associated with contrasts for a factor may
> not be of too much interest by themselves, because they are expressed
> with respect to a somewhat arbitrary reference level for the factor.
> Also these do not take into account multiple comparisons.
>
>
>>
>> Thanks so much for any insights.
>>
>>
>>
>> The output I get is:
>>
>>
>>
>> Generalized linear mixed model fit by the Laplace approximation
>>
>> Formula: birds ~ ownership + (1 | site)
>>
>>    Data: wma
>>
>>    AIC   BIC logLik deviance
>>
>>   171.3 184.7 -81.63    163.3
>>
>> Random effects:
>>
>>   Groups Name        Variance Std.Dev.
>>
>>   site   (Intercept) 0.099663 0.31569
>>
>> Number of obs: 211, groups: site, 36
>>
>>
>>
>> Fixed effects:
>>
>>                      Estimate Std. Error z value Pr(>|z|)
>>
>> (Intercept)            0.1209     0.1497   0.807  0.41947
>>
>> ownershipCrownland     0.5362     0.1977   2.712  0.00669 **
>>
>> ownershipPrivateland   0.3902     0.1956   1.995  0.04608 *
>>
>> ---
>>
>> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>>
>>
>>
>> --
>> Sandra M Durán
>> University of Alberta
>>
>>         [[alternative HTML version deleted]]
>>
>>
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>>
>>
>>
>>
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