Closed gtng92 closed 6 years ago
That statement halts the simulation when the infected subpopulation goes extinct. There is no coalescent process in these simulations -- they are run forward in time. My guess is that the parameter settings are such that the transmission rate is not sufficiently high to sustain the epidemic, at least to the point that you reach the required number of sampled infections.
Ok thanks, that seems to work for higher numbers of nparticles now.
With SMC, there is always a chance that a particle will end up in a silly region of parameter space, so we should have some hard limit to simulation time that we can catch as an exception and return a big distance to spike that particle out of contention.
In the MASTER XML InheritanceTrajectory
specification, use the argument maxConditionRejects
to set a limit to the number of attempts for a particle to generate a tree
Currently setting maxConditionRejects
to 50 before exiting.
Stochastically, usually when
nparticle > 3
, printout from MASTER call becomes infinite:In the current XML template:
Is this because the ancestors never coalesce?