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 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]] >> >> >> _______________________________________________ >> R-sig-mixed-models@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models >> >> >> >> >> _______________________________________________ >> R-sig-mixed-models@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models [[alternative HTML version deleted]]