[R-sig-ME] Time-dependent Negative binomial regression

[Thierry Onkelinx]

Dear Amir,

Have a look at the lme4, glmmTMB or INLA packages. Note that if you need on
the fly transformations in the model you need to code them as
I(log(person.time)) instead of log(person.time). Personally, I prefer to
create a new variable in the data.frame and use that new variable in the
model.

Another thing is that you shouldn't use gender and baseline.age as random
effects. Either don't use them (as their effect is handled by the id random
effect) or add them as fixed effects.

library(lme4)
glmer.nb(event ~ offset(log_time) + treatment + gender + baseline.age +
(1|id), data = df)

Best regards,


ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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Op do 8 jul. 2021 om 08:59 schreef <
Amirhossein.AmirhosseinTalebi using radboudumc.nl>:

> Dear responders,
>
>
> Recently I have processed and cleaned a data for the aim of application of
> a negative binomial regression.
>
> First, I tried to use the function glm.nb of package MASS in R and I had a
> problem with ensuring that the model will realize the data are for one
> unique participant (possible correlations in a group of observations).
>
> Then, I realized that I can use glmmPQL of package MASS or glmer of
> package lme4 and use the family negative binomial in it's family link.
>
> The question is I would like to know in which part of the model I can
> embed the offset (logarithm of the number of days of treatment) also how
> should I insert the time-constant observations for an id (such as gender
> and baseline age in the df)?
>
> My latest attempt was:
>
> (glmmPQL (event ~ treatment + offset (log(person.time)) ,
> random= list (id=~1, gender=~1, baseline.age=~1),
> family= negative.binomial (theta=1.75), data=df ))
>
>
> which faced with a memory-related error (probably because of the wrong
> code). data example:
>
> df<-data.frame(id=rep(1:3,each=4),treatment=sample(c(0,1),12,replace = T),
> event=sample(c(0,1),12,replace = T),
> person.time=sample(c(15,31,30),12,replace = T),
> age=rep(c(65,58,74),each=4),gender=rep(c("m","f","m"),each=4))
>
>
> Thank you for your time and considerations,
>
> Amir
>
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