Problem with frequency trajectory when simulating with large adaptive theta and small selection coefficint

[ngarud]

Hi Greg,

I noticed in both the new and old versions of MSMS that there is a problem with the frequency trajectory of sweeps with large adaptive thetaA values (i.e. around 10 or 20) and small selection coefficients (of around 0.001). In many cases (if not all), the frequency trajectory suddenly jumps and we we see a complete (or near complete) hard sweep. This does not make any sense because the frequency trajectory is not continuous and smooth, and such high thetaA values with small selection coefficients should rarely result in 1 haplotype at very high frequency.

Please let me know if you'd like some code for specific examples that generate these scenarios.

Nandita