Hi,
The first thing to check is if both functions use the same 'base' option - they
usually don't.
On a more general note, the two approaches use a different data augmentation
procedure, but this should not have a very large impact on the results provided
enough draws and similar priors are used. If you want to go more into detail on
what are the exact differences, the Imai and van Dyk (2005) paper is very
useful.
Best regards,
Ana
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