[R-sig-ME] Attention Ben Bolker: Issues with glmer.nb() in R

Mollie Brooks mbrooks at ufl.edu
Tue Sep 27 22:35:53 CEST 2016

Hi Dominique,

It looks like you specified the offset in model1 in the wrong way and that is causing the error.
model1 <- glmer.nb(FishCounts ~ DaysSinceRelease * SizeRanking *
SeededDensity + (1|Site)+(1|SampleRound) +
offset(InitialNumberPerQuadrat),data = x))

Because of the log-link, you probably actually want

Your csv file was removed by the mail server. So I haven’t looked at your data.

You can’t use AIC to choose the best distribution until you’ve fitted models with the various distributions. Use AIC on the fitted models.


> On 27Sep 2016, at 21:27, Dominique Prinsloo <domprinsloo at gmail.com> wrote:
> Hi Ben
> I hope you are well. I have some issues regarding the structure of a GLMM
> in R using the glmer.nb().

> I have posted this question on Cross Validated at this link:
> http://stats.stackexchange.com/questions/237216/how-do-you-structure-a-glmm-using-a-glmer-nb-in-r
> Here is the question and attached is a csv. file with a sample dataset.
> I want to find out what variable affects the number of fish counts.
> FishCounts is my response variable and it needs to be offset by the
> InitialNumberPerQuadrat. I have three fixed effects that I want to test:
> DaysSinceRelease, SizeRanking and SeededDensity or the interactions between
> them. There are 18 sites and each Site was sampled up to 3 times (
> SampleRound 1, 2 or 3) in the period of 600 days, therefore my random
> variables need to take into account the repeated measures. The most
> appropriate distribution for my response variable was the Negative Binomial
> distribution as it had the lowest AIC value.
> Firstly, should i use glmer() and then stipulate family=negative.binomial?
> Or should I use glmer.nb()?
> I have tried both ways but the glmer.nb() allows me to offset my variable
> which is what I need to do. So have I structured the code correctly? Are
> the random variables correct and do they account for the repeated measures?
> model1 <- glmer.nb(FishCounts ~ DaysSinceRelease * SizeRanking *
> SeededDensity + (1|Site)+(1|SampleRound),
> offset(InitialNumberPerQuadrat),data = x))
> When I run this code, I keep getting the following error: 'control' is not
> a list; use glmerControl()?
> Please help me as i'm getting desperate to figure this out.
> Thanks
> Dominique
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