[R-sig-ME] Convergence diagnostics for MCMCglmm

[Dawson Wayne]

That's great, thought the lists to use might have been $Sol, but hey,  
that just seemed too simple!

Thanks Jarrod and Ben.

Wayne

Quoting Jarrod Hadfield <j.hadfield at ed.ac.uk>:

> Hi Wayne,
>
> You should pass the mcmc objects from >2 models as a list. For  
> example, the fixed effects:
>
> diag.gelman(mcmc.list(m1$Sol, m2$Sol))
>
> Ideally the models should have over-dispersed starting values, which  
> you can specify in the start argument. This will stop MCMCglmm  
> finding "heuristically" good starting values.
>
> If you have access to ASReml you could always fit the model using  
> REML and check to see whether the estimates are the same/similar.
>
> Cheers,
>
> Jarrod
>
>
> On 19 Nov 2009, at 13:20, Dawson Wayne wrote:
>
>> Dear R users,
>>
>> I've managed to get to grips with using MCMCglmm for phylogenetic  
>> meta-analysis, thanks to help on here from Jarrod Hadfield.  
>> However, I haven't yet worked out how to use convergence  
>> diagnostics on MCMCglmm output.
>>
>> I am currently running models for 50,000 iterations, with a long  
>> burnin of 25000, and a thinning interval of 10. Whilst my trace  
>> plots look good, I would like to use the Gelman-Rubin or  
>> Raftery-Lewis diagnostics in the coda package to check that my  
>> burnin/no. of iterations are adequate. I've read relevant sections  
>> in Ch. 7 of Ben Bolkers ecological models book, and the  
>> coda/MCMCglmm package pdfs, but I'm still not sure what mcmc output  
>> from MCMCglmm I am supposed to pass to the coda diagnostic  
>> functions. Apologies for the simple question, but hopefully there  
>> is a simple answer!
>>
>> Any suggestions appreciated as always,
>>
>> Thanks,
>>
>> Wayne
>>
>> -- 
>> Dr. Wayne Dawson
>> Institute of Plant Sciences
>> University of Bern
>> Altenbergrain 21
>> 3013 Bern
>> Switzerland
>> +41 (0)31 631 49 25
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
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>>
>
>
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>



-- 
Dr. Wayne Dawson
Institute of Plant Sciences
University of Bern
Altenbergrain 21
3013 Bern
Switzerland
+41 (0)31 631 49 25