Convergence issues had been an identifiability problem.  Was going to an initial state with non-zero recovereds.  I fixed this here by adding a likelihood to the model that prefers zero recovereds.  However, this is causing massively slow mixing, because changing any one of the epidemiological parameters pushes the initial recovereds off their mark.  Will attempt to move to a forward-simulation approach.
Convergence issues had been an identifiability problem.  Was going to an initial state with non-zero recovereds.  I fixed this here by adding a likelihood to the model that prefers zero recovereds.  However, this is causing massively slow mixing, because changing any one of the epidemiological parameters pushes the initial recovereds off their mark.  Will attempt to move to a forward-simulation approach.

git-svn-id: 67bc77c75b8364e4e9cdff0eb6560f5818674cd8@4596 ca793f91-a31e-0410-b540-2769d408b6a1

armanbilge/BEAST_sandbox,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,svn2github/beast-mcmc,armanbilge/BEAST_sandbox