Hi Joshua,
Thank you for your response. I do have those Course Notes, but only skimmed
the technical details b/c I don't have any RE. I'll look further into it.
Thank you for looking into extracting the proposal variance, I don't have
enough knowledge to look into or understand the guts of most programs,
especially if they're in C. I know I can provide a proposal distribution,
that's the entire point. I want to run this model for enough iterations
such that the proposal distribution is "good" in that the acceptance rate
is ~25% or so. Then I want to know what that proposal distribution is, so I
can restart the model using this good proposal distribution with no burnin.
This probably sounds strange, but this model is only a step in a larger
cyclical algorithm (Sequential Regression Multiple Imputation (Raghunathan
2001)) that models multiple variables, one iteration at a time. Y1 is
modeled, its results fed into the model for Y2, both those results are fed
into Y3.... until the results from Y2-Yp are fed back into a model for Y1.
So I need to draw 1 iteration at a time using a a constant proposal
distribution that does not adapt.
I was just hoping to avoid those re-calculations this time and have
MCMCglmm just tell me what a good proposal variance was instead of having
to figure it out myself :)
FYI, The small priors were not intentional, essentially a typo. Thank you
for pointing it out.
Anyhow, thank you again for helping me figure out how I'm going to do what
i need to do. I appreciate the time you spent on it.
-Robin
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