[R-sig-ME] Convergence diagnostics for MCMCglmm

Dawson Wayne wayne.dawson at ips.unibe.ch
Thu Nov 19 14:20:27 CET 2009

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  

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,



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

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