Update Stan model and sim testing

WGGRAFY / sarla

State space autoregressive length-at-age model

0 stars 1 forks source link

Update Stan model and sim testing #2

Closed seananderson closed 3 years ago

seananderson commented 3 years ago

Match simulation and fitting and make plots
Try to match annual anomalies version from CJFAS paper... should be easy to extend to the other options from here
Add log_lik for LOOIC for comparing across the various setups
Add posterior predictive samples

Convergence isn't fantastic once I added the annual anomalies. I think we're pushing the estimation here, but it still seems doable.

seananderson commented 3 years ago

I've drawn the initial year and age matrix values from a Normal(0, 1), but it looks like you had estimated that variance separately before. Anyways, hopefully we can build from here.