Re: [R-sig-eco] Mixed model with zero truncated Poisson distributed data

[Mollie Brooks]

Hi Helen,
The package MCMCglmm can fit a zero truncated Poisson by specifying 
family="ztpoisson"
After installing and loading the package, a good place to start it the pdf 
brought up by
vignette("CourseNotes")
best,
Mollie

Mollie Brooks
Ph.D. Candidate
NSF IGERT Fellow
Biology Department
University of Florida
mbro...@ufl.edu
http://people.biology.ufl.edu/mbrooks




On 11 Jan 2012, at 10:58 AM, Helen Ward wrote:

> Hello,
> 
> I am a PhD student currently trying to derive a mixed effects model.
> 
> I would like to describe the relationship between age and male 
> reproductive success in a population of greater horseshoe bats.
> 
> My data consists of three columns: MaleID, Age, NumberofPups (at that 
> age). Many of the males appear multiple times in the data set, so I 
> believe I need to derive a mixed model with MaleID as a random variable.
> 
> The data is Poisson distributed, but zero-truncated. So far I have only 
> succeeded in making a mixed model with a poisson distribution (using 
> glmmPQL in the MASS package), and a zero truncated poisson model (using 
> vglm in the VGAM package), but not a mixed model capable of handling 
> zero truncated Poisson data.
> 
> It has been suggested that I could just minus 1 from each value in the 
> NumberofPups column to make a more usual Poisson distribution, so I can 
> ignore the zero truncated bit. I have tried this and it changes the 
> results of the model, but is this an acceptable transformation?
> 
> If not, can anyone advise me on a mixed model that can handle zero 
> truncated Poisson data please?
> 
> I also intend to post this on the R-sig-mixed-models 
> 
>  
> list, so apologies if you've seen it twice!
> 
> Many thanks,
> Helen
> 
> 
>   [[alternative HTML version deleted]]
> 
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> 

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Re: [R-sig-eco] Mixed model with zero truncated Poisson distributed data

[Bob O'Hara]

On 01/11/2012 04:58 PM, Helen Ward wrote:

Hello,

I am a PhD student currently trying to derive a mixed effects model.

I would like to describe the relationship between age and male
reproductive success in a population of greater horseshoe bats.

My data consists of three columns: MaleID, Age, NumberofPups (at that
age). Many of the males appear multiple times in the data set, so I
believe I need to derive a mixed model with MaleID as a random variable.

The data is Poisson distributed, but zero-truncated. So far I have only
succeeded in making a mixed model with a poisson distribution (using
glmmPQL in the MASS package), and a zero truncated poisson model (using
vglm in the VGAM package), but not a mixed model capable of handling
zero truncated Poisson data.

It has been suggested that I could just minus 1 from each value in the
NumberofPups column to make a more usual Poisson distribution, so I can
ignore the zero truncated bit. I have tried this and it changes the
results of the model, but is this an acceptable transformation?

If not, can anyone advise me on a mixed model that can handle zero
truncated Poisson data please?

I also intend to post this on the R-sig-mixed-models

list, so apologies if you've seen it twice!

If an individual would have had pups, would you have seen it?

I'm wondering if you could simply add the zeroes back into the data.

Bob

--

Bob O'Hara

Biodiversity and Climate Research Centre
Senckenberganlage 25
D-60325 Frankfurt am Main,
Germany

Tel: +49 69 798 40216
Mobile: +49 1515 888 5440
WWW:   http://www.bik-f.de/root/index.php?page_id=219
Blog: http://blogs.nature.com/boboh
Journal of Negative Results - EEB: www.jnr-eeb.org

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[R-sig-eco] Mixed model with zero truncated Poisson distributed data

[Helen Ward]

Hello,

I am a PhD student currently trying to derive a mixed effects model.

I would like to describe the relationship between age and male 
reproductive success in a population of greater horseshoe bats.

My data consists of three columns: MaleID, Age, NumberofPups (at that 
age). Many of the males appear multiple times in the data set, so I 
believe I need to derive a mixed model with MaleID as a random variable.

The data is Poisson distributed, but zero-truncated. So far I have only 
succeeded in making a mixed model with a poisson distribution (using 
glmmPQL in the MASS package), and a zero truncated poisson model (using 
vglm in the VGAM package), but not a mixed model capable of handling 
zero truncated Poisson data.

It has been suggested that I could just minus 1 from each value in the 
NumberofPups column to make a more usual Poisson distribution, so I can 
ignore the zero truncated bit. I have tried this and it changes the 
results of the model, but is this an acceptable transformation?

If not, can anyone advise me on a mixed model that can handle zero 
truncated Poisson data please?

I also intend to post this on the R-sig-mixed-models 
 
list, so apologies if you've seen it twice!

Many thanks,
Helen


[[alternative HTML version deleted]]

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