Issues with jt_mcmc.c

[nichole-carlson]

This is the overall program for calling the mcmc. It needs a correct function call for outputting to the screen and files.

[nichole-carlson]

The intro parts to the program will become embedded into the new MH routine. Where should proposal variance initialization go because that is what is happening prior to the big MCMC loop.

[nichole-carlson]

Why the MCMC ordering that is in the program. What order should parameters be drawn. Maybe move the function calls to a different order.

[nichole-carlson]

Check brackets at the end of the code.

[nichole-carlson]

Need to embed the acceptance updates (adaptive MH) into each MH routine. I think this is being done in the class for the pop model