[R-sig-ME] Quasi Poisson for glmm

[Ebhodaghe Faith]

Many thanks to you both, Thierry and Ben for your kind responses, which I
find really helpful.

Regards
Faith

On Thu, 3 Dec 2020 8:31 pm Ben Bolker, <bbolker using gmail.com> wrote:

>     I agree with Thierry that the binomial is a good start.
>
>     If you do find that there is overdispersion in your binomial model,
> there are (at least) three possible approaches (see
> http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#overdispersion ):
>
>    * beta-binomial model
>    * observation-level random effects in a binomial model
>    * quasi-binomial
>
>    The last one is not available in glmmTMB, but the GLMM FAQ
> http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html shows you how to
> get quasi-likelihood results if you want.
>
>    cheers
>      Ben Bolker
>
>
> On 12/3/20 10:55 AM, Thierry Onkelinx via R-sig-mixed-models wrote:
> > Dear Faith,
> >
> > I'd recommend starting with a full model with binomial distribution. What
> > you perceive as overdispersion in the response is often modelled by the
> > covariates.
> >
> > 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
> >
> >
> ///////////////////////////////////////////////////////////////////////////////////////////
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> say
> > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > The plural of anecdote is not data. ~ Roger Brinner
> > The combination of some data and an aching desire for an answer does not
> > ensure that a reasonable answer can be extracted from a given body of
> data.
> > ~ John Tukey
> >
> ///////////////////////////////////////////////////////////////////////////////////////////
> >
> > <https://www.inbo.be>
> >
> >
> > Op do 3 dec. 2020 om 16:17 schreef Ebhodaghe Faith <
> ebhodaghefaith using gmail.com
> >> :
> >
> >> Dear Thierry,
> >> The proportions are on number of individuals infected by a parasite
> >> divided by total number of individuals examined.
> >>
> >> Thanks
> >> Faith
> >>
> >> On Thu, 3 Dec 2020, 4:48 p.m. Thierry Onkelinx, <
> thierry.onkelinx using inbo.be>
> >> wrote:
> >>
> >>> Dear Faith,
> >>>
> >>> I missed to see you have a proportion response. The negative binomial
> is
> >>> a (better) alternative for the quasi Poisson. But they assume count
> data.
> >>> What kind of proportions do you have? Is it based on a number of
> >>> successes for a number of trials (binomial, beta binomial)? Or a
> continuous
> >>> value between 0 and 1 (beta)?
> >>>
> >>> 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
> >>>
> >>>
> >>>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >>> To call in the statistician after the experiment is done may be no more
> >>> than asking him to perform a post-mortem examination: he may be able
> to say
> >>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> >>> The plural of anecdote is not data. ~ Roger Brinner
> >>> The combination of some data and an aching desire for an answer does
> not
> >>> ensure that a reasonable answer can be extracted from a given body of
> data.
> >>> ~ John Tukey
> >>>
> >>>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >>>
> >>> <https://www.inbo.be>
> >>>
> >>>
> >>> Op do 3 dec. 2020 om 13:14 schreef Ebhodaghe Faith <
> >>> ebhodaghefaith using gmail.com>:
> >>>
> >>>> Thanks, Thierry.
> >>>>
> >>>> But could you please refer me to an article preferably in the
> biological
> >>>> sciences where a negative binomial distribution was used to model an
> >>>> over-dispersed multilevel proportion response variable?
> >>>>
> >>>> Thanks for your kind assistance.
> >>>>
> >>>> Regards
> >>>> Faith
> >>>>
> >>>> On Thu, 3 Dec 2020, 1:32 p.m. Thierry Onkelinx, <
> >>>> thierry.onkelinx using inbo.be> wrote:
> >>>>
> >>>>> Dear Faith,
> >>>>>
> >>>>> You can use a negative binomial distribution.
> >>>>>
> >>>>> 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
> >>>>>
> >>>>>
> >>>>>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >>>>> To call in the statistician after the experiment is done may be no
> more
> >>>>> than asking him to perform a post-mortem examination: he may be able
> to say
> >>>>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> >>>>> The plural of anecdote is not data. ~ Roger Brinner
> >>>>> The combination of some data and an aching desire for an answer does
> >>>>> not ensure that a reasonable answer can be extracted from a given
> body of
> >>>>> data. ~ John Tukey
> >>>>>
> >>>>>
> ///////////////////////////////////////////////////////////////////////////////////////////
> >>>>>
> >>>>> <https://www.inbo.be>
> >>>>>
> >>>>>
> >>>>> Op do 3 dec. 2020 om 11:24 schreef Ebhodaghe Faith <
> >>>>> ebhodaghefaith using gmail.com>:
> >>>>>
> >>>>>> Hi All.
> >>>>>>
> >>>>>> I have a dataset for wish I intend to model an over-dispersed
> >>>>>> proportion
> >>>>>> response variable with hierarchical structure. I tried using the
> Quasi
> >>>>>> Poisson family, but available packages including glmmTMB do not
> allow
> >>>>>> this.
> >>>>>> What do you advice?
> >>>>>>
> >>>>>> Thanks in advance for your kind response.
> >>>>>>
> >>>>>> Faith Ebhodaghe
> >>>>>> Nairobi, Kenya
> >>>>>>
> >>>>>>          [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> R-sig-mixed-models using r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>>>>>
> >>>>>
> >
> >       [[alternative HTML version deleted]]
> >
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> >
>
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