profile and/or bootstrapped CIs for GAMM random effects
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This looks like it could get ugly, we might have to call on Simon Wood. I've posted it as https://github.com/lme4/lme4/issues/333 , but I think it's really a gamm4 problem or at least a gamm4/lme4 communication problem. The part of the problem I've been able to identify so far is that the @call slot of the $mer part of the gamm4 object does *not* look like a normal lme4 call, which causes problems (much farther down) where we use update() to try to reconstruct a version of the model that is just a deviance function. Getting a deviance function back from a glmerMod object in a more straightforward way is something that's been on our list ... Ben Bolker
On 15-09-01 06:51 PM, John Morrongiello wrote:
Hi all I thought I'd re-post this message from last week as it may have got lost in the weekend traffic: I'm having trouble estimating CIs for random effects (i.e. CODE) from a gamm4 model fit with a gamma distribution, My model is: c1<-gamm4((longdist)~s(time,k=4),random=~(1|CODE),data=catfish1,family=Gamma(link=log))
confint(c1$mer,method="profile")
##this returns Error in mkMerMod(rho = environment(devfun), opt = opt, reTrms = b$reTrms, : unused argument (devFunOnly = TRUE) confint(c1$mer,method="boot") ##this returns Error in mkNewReTrms(object, newdata, compReForm, na.action = na.action, : random effects specified in re.form that were not present in original model Are these errors arising because I'm using a gamma distribution? Is there another way to get the random effect CIs? I can get random effect CIs for the following model: c2<-gamm4((longdist)~s(time,k=4),random=~(1|CODE),data=catfish1,family=gaussian) confint(c2$mer,method="profile")##works confint(c2$mer,method="boot")##same error message as above Thanks for your time John -- Dr. John R. Morrongiello School of BioSciences University of Melbourne Victoria 3010, Australia T: +61 3 8344 8929 M: +61 403 338 554 E: john.morrongiello at unimelb.edu.au<mailto:%20jmorrongiell at unimelb.edu.au>
W: morrongiellolab.com<http://morrongiellolab.com/>
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