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rBatt / trawl

Analysis of scientific trawl surveys of bottom-dwelling marine organisms
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Reduce data augmentation? #86

Closed rBatt closed 8 years ago

rBatt commented 8 years ago

To determine richness you don't have to sum Z over the augmented indices. Data augmentation is used not just to get asymptote (sum Z over all indices), but to just get stability in the parameter distributions. Might be worth reducing augmentation to see if I can get the same answer (reducing augmentation has the advantage of reducing the computation demand of model fitting).

rBatt commented 8 years ago

During simulation testing, I'm not noticing a lot of benefit to adding a ton of 0 species. Mainly, it just seems to slow things down. @mtingley what's your approach to choosing 0's?

mtingley commented 8 years ago

Depends. Some analyses I don't use data augmentation. In a multi-year study where you have a good idea of the true meta community it seems to make sense to keep augmentation limited.

rBatt commented 8 years ago

Fair enough. That at least isn't a sharp contrast with my impression.

I'm going to try my hand at the dynamic model next week. I still don't quite understand this distinction between colonizing, occupying, and persisting. I mean, the distinction in common language is clear to me, but I guess I don't fully understand why you would bother to model them as separate processes.

As I say that, I guess it's because you might think different processes affect occupancy depending on whether or not it was there the previous time step. If your species is a boulder, occupancy probability is low if the boulder wasn't there the last time step (boulders don't just show up out of nowhere very often), and the boulder has a high probability of occupancy if it was there the previous time step, because boulders don't just disappear.

I digress. Thanks.

On Friday, December 4, 2015, Morgan Tingley notifications@github.com wrote:

Depends. Some analyses I don't use data augmentation. In a multi-year study where you have a good idea of the true meta community it seems to make sense to keep augmentation limited.

— Reply to this email directly or view it on GitHub https://github.com/rBatt/trawl/issues/86#issuecomment-162136950.

rBatt commented 8 years ago

In my testing/ playing I've been keeping the augmentation tiny. Like 2 species.

rBatt commented 8 years ago

I'm currently getting good convergence with 50 'zero' species. Omega is not bumping up against 1.

It was important to scale all of the covariates to mean 0 and sd 1.