[R-sig-ME] Problem with bootMer and models with offset

[Ben Bolker]

Martin Hecht <martin.hecht at ...> writes:

> 
> 
> Hi,
> 
> I am using the latest version of R (3.1.1) and lme4 (1.1-7) .
> 
> I'm getting some weird implausible bootstrap results from bootMer for a
> model with an offset (models without offset work fine).
> 
> I've attached an Rdata file with the returned object from lmer (lmerObj)
> and the returned object from bootMer (booted)

  Unfortunately, Rdata/RData files get stripped by the mailing list
software (there's a short list of attachments that get allowed --
I'm not sure how to find it -- probably includes txt and CSV files
but not much else).

> Any help would be appreciated very much.
> 
> the syntax is:
> 
> booted <- bootMer ( x = lmerObj , FUN =
> function(fit){return(c(fixef(fit),getME(fit,'theta')))} , nsim = 100 ,
> seed = 65835 , verbose = TRUE )
> 
> > booted$t0[1]
> (Intercept)
>     2.606621
> 
> > mean(booted$t[,1])
> [1] -78.21035
> 
> > boot::boot.ci ( booted , conf = 0.95 , type = "basic" , index = 1 )
> BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
> Based on 100 bootstrap replicates
> 
> CALL :
> boot::boot.ci(boot.out = booted, conf = 0.95, type = "basic",
>     index = 1)
> 
> Intervals :
> Level      Basic        
> 95%   (69.864, 95.425 ) 
> Calculations and Intervals on Original Scale
> Some basic intervals may be unstable

  This does indeed seem weird.

  Does plot(booted,1) help at all?

  I wonder if a workaround for now is to add the offset manually;
that should be perfectly feasible (if not quite as convenient)
for a linear mixed model -- it's only really *necessary* for
a GLMM ...