Calculate MCMC diagnostics?
then the MCMC diagnostics window will appear, and if you click on the Diagnostic Settings button at the bottom of this window you will see a box at the bottom of the window that appears, with Increase burn-in length by next to it. Type in here the iteration number up to which you want the burn-in period to run (this will give a burn-in length of the number you type in plus the burn-in length you were already using to run MCMC) and click Apply and Done. The ‘posterior mean’ estimate in the MCMC diagnostics window is now the parameter estimate under this longer burn-in and the ‘SD’ is the standard error of the parameter estimate. You can now click on the trajectory graph for any other parameter and the ‘posterior mean’ and the ‘SD’ will be adjusted to take into account the longer burn in (i.e. you do not need to click the Diagnostic Settings button for all the other parameters). Note however that the estimates displayed above the trajectory graphs in the Trajectories window will not be u
