popsim-consortium / analysis

Analysis of inference methods on standard population models

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Demographic inference methods to apply #1

Open arundurvasula opened 5 years ago

arundurvasula commented 5 years ago

We talked about gathering a list of methods to apply to the simulations on the call today

squiggly line

MSMC
stairway plot
SMC++

multipopulation

dadi
fastsimcoal
momi
GPhocs

Please comment on additions! Not sure where we should keep the final list.

andrewkern commented 5 years ago

so @cjbattey has code to lend for running stairway plot and SMC++, we are going to push ahead writing some code for starting this analysis. @jeromekelleher @petrelharp did we settle on a name for the new repo for analysis?

jeromekelleher commented 5 years ago

@jeromekelleher @petrelharp did we settle on a name for the new repo for analysis?

Nope. Shall we just call it 'analysis' and be done?

andrewkern commented 5 years ago

fine by me.

jeromekelleher commented 5 years ago

OK, done. Moving this issue over there.

andrewkern commented 5 years ago

Question-- should we organize analysis by method or by organism?

jeromekelleher commented 5 years ago

Question-- should we organize analysis by method or by organism?

What about by "thing-we're-trying-to-estimate"? That would map well into sections for the paper then.

petrelharp commented 5 years ago

Not sure: how much organism- and method-specific code is there? We probably have to do an example or two to see.

andrewkern commented 5 years ago

check out what I sketched up here

petrelharp commented 5 years ago

It was proposed in the meeting just now to add msmc to the multiple population list also.

andrewkern commented 5 years ago

yes and Kirk and company have volunteered to fun fastsimcoal2 for us. Thanks guys!