[R-sig-ME] Mixed model for count data with overdispersion

[Christopher David Desjardins]

Hi,

You really should read about the MCMCglmm package before just using it. There are a couple of vignettes which I strongly suggest that you read prior to actually using MCMCglmm as they explain a lot.

https://cran.r-project.org/web/packages/MCMCglmm/vignettes/Overview.pdf <https://cran.r-project.org/web/packages/MCMCglmm/vignettes/Overview.pdf>
https://cran.r-project.org/web/packages/MCMCglmm/vignettes/CourseNotes.pdf <https://cran.r-project.org/web/packages/MCMCglmm/vignettes/CourseNotes.pdf>

Do note that you need to specify prior distributions or at least understand the default ones.

Chris

> On Aug 10, 2015, at 8:56 AM, Mehdi Abedi <abedimail at gmail.com> wrote:
> 
> Thanks Manabu,
> It is a bit complicated for me but If i have this data:
> Parameter: Totalseedling
> fixed effect: Heatsmoke, cold
> random effect: plot
> 
> I should do something like this?!
> 
> 
> Model1<- MCMCglmm(Totalseedling ~ Heatsmoke *Cold, random =
> ~Plots,family="poisson", data = growthdata)
> summary( Model1)
> It looks i can not get anova() here for output as well?
> 
> 
> I am not familiar with other details in the MCMCglmm:
> 
> library( MCMCglmm)
> Model1<- MCMCglmm(Totalseedling ~ Heatsmoke *Cold, random = ~Plot,
> + family = "poisson", data = growthdata, prior = prior,
> + verbose = FALSE, pr = TRUE)
> 
> Warm regards,
> Mehdi
> 
> On Mon, Aug 10, 2015 at 12:48 PM, Manabu Sakamoto <manabu.sakamoto at gmail.com <mailto:manabu.sakamoto at gmail.com>
>> wrote:
> 
>> Dear Mehdi,
>> 
>> You can use the function MCMCglmm in the package of the same name,
>> specifying family="poisson". MCMCglmm automatically accounts for over
>> dispersion in count data.
>> 
>> best regards,
>> Manabu
>> 
>> On 10 August 2015 at 06:54, Mehdi Abedi <abedimail at gmail.com> wrote:
>> 
>>> Dear all,
>>> 
>>> I had quick search but it looks there is no simple way in lme4 or  nlme In
>>> the case of overdispersion for count data,. How we can run mixed model for
>>> count data with family of quasipoisson or maybe NB?
>>> 
>>> I my working on seeding emergence with 2 fixed factor (n=10) and i would
>>> like to have my plot as replicate(n=5) as a random.
>>> 
>>> Warm regards,
>>> Mehdi
>>> 
>>> --
>>> 
>>> 
>>> *Mehdi Abedi Department of Range Management*
>>> 
>>> *Faculty of Natural Resources & Marine Sciences *
>>> 
>>> *Tarbiat Modares University (TMU) *
>>> 
>>> *46417-76489, Noor*
>>> 
>>> *Mazandaran, IRAN *
>>> 
>>> *mehdi.abedi at modares.ac.ir <Mehdi.abedi at modares.ac.ir>*
>>> 
>>> *Homepage
>>> <http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>*
>>> 
>>> *Tel: +98-122-6253101 *
>>> 
>>> *Fax: +98-122-6253499*
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
>>> _______________________________________________
>>> R-sig-mixed-models at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> 
>> 
>> 
>> 
>> --
>> Manabu Sakamoto, PhD
>> manabu.sakamoto at gmail.com
>> 
> 
> 
> 
> -- 
> 
> 
> *Mehdi Abedi Department of Range Management*
> 
> *Faculty of Natural Resources & Marine Sciences *
> 
> *Tarbiat Modares University (TMU) *
> 
> *46417-76489, Noor*
> 
> *Mazandaran, IRAN *
> 
> *mehdi.abedi at modares.ac.ir <mailto:mehdi.abedi at modares.ac.ir> <Mehdi.abedi at modares.ac.ir <mailto:Mehdi.abedi at modares.ac.ir>>*
> 
> *Homepage
> <http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi <http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>>*
> 
> *Tel: +98-122-6253101 *
> 
> *Fax: +98-122-6253499*
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-sig-mixed-models at r-project.org <mailto:R-sig-mixed-models at r-project.org> mailing list
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