search

gchen98 / macs

Automatically exported from code.google.com/p/macs
16 stars 6 forks source link

units of exponential growth #35

Closed agladstein closed 7 years ago

agladstein commented 7 years ago

Hi Gary,

I'm using macs to run simulations for Approximation Bayesian Computation to infer demographic parameters. Part of my model is exponential growth. I'm confused about what units the growth rate parameter is in. Take a look at this overleaf for more details on my question. https://www.overleaf.com/9631592trgnjyzqfhvz

Thanks, Ariella

gchen98 commented 7 years ago

Hi Ariella,

Sorry for the delay. I haven't been in touch with the software in quite a long time. And to make matters worse, I left academia about two years ago for a completely different field.

Nevertheless, I tried to preserve as much as possible from the ms code as possible, as far as time units (e.g. 4Ne generations) and other equations go. Does page 8 from https://snoweye.github.io/phyclust/document/msdoc.pdf help? You may also want to tap Jeff Wall's brain as well, since he probably still uses the software from time to time.

Gary

agladstein commented 7 years ago

Hi Gary,

Thanks for the reply anyways. I figured it out (with some help). Growth rate should be in coalescent units (4Ne generations).

screen shot 2017-05-22 at 8 09 24 am
gchen98 commented 7 years ago

4Ne (our time unit for the coalescent) would have been my original response (as I alluded to in my previous message) but somehow I thought you were asking for something a bit more complicated. :)

agladstein commented 7 years ago

Nope! It just wasn't clear to me from the manual or from any papers that use ms/macs. Numerically, units of 4Ne didn't make sense with the growth estimates given by Carmi et al. 2014 (but, that was because they used a factorial exponential growth model, not the same exponential growth ms/macs uses).

On Mon, May 22, 2017 at 8:51 AM, Gary K. Chen notifications@github.com wrote:

4Ne (our time unit for the coalescent) would have been my original response (as I alluded to in my previous message) but somehow I thought you were asking for something a bit more complicated. :)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gchen98/macs/issues/35#issuecomment-303140865, or mute the thread https://github.com/notifications/unsubscribe-auth/AZYk_lftu9mQl0bHY9vbx83XgUlxhJd2ks5r8a72gaJpZM4Nf-YT .

-- Ariella Gladstein Ecology and Evolutionary Biology Graduate Program University of Arizona agladstein@email.arizona.edu