Help improving a fisheries state space model with biased estimation

[spinkney]

I don’t have the time to really dive in to this model. But you can try an extended Kalman filter (see Extended Kalman filter, problem estimating process and observation error size) where you work out the Jacobians (I believe you can work those out analytically from the model given). Unfortunately, there’s no built-in function to take those derivatives so you have to write them yourself. There’s an example in the linked post.