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petrelharp / context

Context-dependent mutation rate inference machinery.
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investigate multiple peaks in likelihood surface #35

Open matsen opened 9 years ago

matsen commented 9 years ago

Want to investigate the multiple peaks thing? Simulate one set of data, start a bunch of optimizations from different starting points? You'll have to make sure the scaling parameters are reasonable, first.

@petrelharp , do you have some systematic exploration of starting points in mind, or were you thinking of just randomly perturbing the starting points used for simulation, say, multiplicatively?

WRT scale, it looks like the code will fill in something if I don't provide parameters. Were you saying that I should make sure that these were reasonable?

petrelharp commented 9 years ago

I didn't have anything in particular in mind; randomly mutplicatively sounds good.

I have disabled the automatic filling in of starting scale parameters (in fit-model.R the code is wrapped in if (FALSE); kept it there so we can move it to a standalone script). So, you'll have to provide parameters.