[R-sig-ME] error with parametric bootstrap for negative binomial model, lme4, pbkrtest

[Leithen]

That looks perfect. Someone will definitely respond!

On Thu, May 21, 2015 at 10:07 AM, Lauren Catherine Ponisio <
lponisio at gmail.com> wrote:

> Hello list members,
> I was hoping to use the a parametric bootstrap using the pbktest package,
> PBmodcomp() function. With a negative binomial mixed model I get the
> following error:
>
> Error in lme4::.simulateFun(object = sm, nsim = nsim, seed = seed) : could
> not find function "sfun"
>
> I get the same error when I try to use the function simulate() on a
> negative binomial model. With other families I do not get an error.
>
> I found that Ben Bolker recommended a hack on the lme4 github site, but I
> cannot get it to work.
> https://github.com/lme4/lme4/issues/284
>
> If fact, below is the code he suggested which gives me the above error.
>
> library(lme4)
> library(pbkrtest)
>
> set.seed(101)
> dd <- data.frame(f=factor(rep(1:10, each=50)),
>                  x=runif(500),
>                  y=rnbinom(500, size=2, mu=2))
>
> g1 <- glmer.nb(y ~ x + (1|f), data=dd)
> g0 <- glmer.nb(y ~ 1 + (1|f), data=dd)
>
> PBmodcomp(g1, g0, nsim=10)
>
> Thanks!
> best,
> Lauren
>



-- 
Leithen M'Gonigle
Assistant Professor
Department of Biological Science
Florida State University
319 Stadium Dr, Tallahassee, FL, 32306
Phone (office): +1 (850) 645-9532
Email: lmgonigle at bio.fsu.edu
Web: http://www.bio.fsu.edu/~lmgonigle/

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