Demographic inference methods to apply

[arundurvasula]

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]

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]

@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]

fine by me.

[jeromekelleher]

OK, done. Moving this issue over there.

[andrewkern]

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

[jeromekelleher]

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]

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

[andrewkern]

check out what I sketched up here

[petrelharp]

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

[andrewkern]

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