[R-sig-ME] Setting priors for binary fixed effects

Yannis Dim. jd|mopou|o@21 @end|ng |rom gm@||@com
Tue Sep 8 08:48:01 CEST 2020

Dear everyone,

I have a comparative phylogenetic model with a binary response variable, 5
binary explanatory variables as fixed effects and the phylogeny as a random
effect. The issue I have is that with a nitt=300,000,000, I check the
heidel.diag(mcmc.list(model$Sol)) and the plot(model) and  the model does
not converge. All the variables pass the Stationarity test but 2 of them
fail the Halfwidth test. The same 2 variables also have bad trace plots.
I wonder if changing the priors will improve the convergence.Currently I
use these priors:
prior<-list(R=list(V=1, fix=1),G=list(G1=list(V=1, nu=1000, alpha.mu=0,

As you can see, I am using the default priors for the fixed effects.

Should I change them, due to the binary nature of my fixed effects? What's
the best priors for binary fixed effects?

I will be immensely grateful if someone could help, as this issue's been
bothering me for some time now.

Kind regards,
Yannis Dimopoulos
PhD Student - The University of Hull

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