Allow halting conditions

[trvrb]

Each timestep look at genetic diversity, quit simulation if greater than some number.

[trvrb]

@sarahCobey do we really need this? I would think explosive diversity would be a proper model output under some regimes.

[sarahCobey]

I like to think of it as a cutoff for what constitutes 'explosive.' In my
experience, running the sim under this regime can take an extremely long
time if the diversity continues to expand. Your call, though.

On Sunday, February 16, 2014, Trevor Bedford notifications@github.com
wrote:

@sarahCobey https://github.com/sarahCobey do we really need this? I
would think explosive diversity would be a proper model output under some
regimes.

Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-35212569
.

[trvrb]

@sarahCobey @OanaCarja I'd like to implement this, but need a good definition of explosive. Do we just look at genealogical diversity? Do we need to consider antigenic diversity as well? Two branches (a single bifurcation event) will have very high genealogical diversity, but should be alright from a computational standpoint.

[sarahCobey]

Shouldn't genealogical diversity be enough? Say, if neTau is extremely high
after some initial burn-in period? (I've noticed it can spike initially in
flu-like simulations.)

On Tue, May 20, 2014 at 4:49 PM, Trevor Bedford notifications@github.comwrote:

@sarahCobey https://github.com/sarahCobey @OanaCarjahttps://github.com/OanaCarjaI'd like to implement this, but need a good definition of explosive. Do we
just look at genealogical diversity? Do we need to consider antigenic
diversity as well? Two branches (a single bifurcation event) will have very
high genealogical diversity, but should be alright from a computational
standpoint.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-43687956
.

[trvrb]

Attack rate? Time profiling? Memory profiling?