Status of setup-utils.R

[lentinj]

I'm working on a Redfish model with Mikko, which has a forked copy of setup-utils.R, which made it's way from the Greenland halibut model.

But looking at the bling model, things have moved on. Do you still use it @willbutler42 ?

https://github.com/gadget-framework/gadget-models/blob/master/07-bling/gadget3%20-%20WKBDEEP/00-setup/setup-model.R

I'm wondering whether I should try to rework the code to use gadgetutils::model_actions instead of the fork, or do something more similar to bling. My instinct is the latter, but it'd be good to know which you prefer atm.

Either way, there's various helpers that'd be worth making their way into the gadget3 package at some point.

[willbutler42]

I strongly recommend going down the blue ling route. Everything setup-utils and model_actions do is now covered much more efficiently (and elegantly) by g3_parameterized. The only reason they are still there is because they are still used for three benchmarked stocks, but I should add a depreciated note to the functions.

I use copies of this helper and this one quite a lot to reduce the number of estimated parameters in the initial conditions (which I guess may be useful for Mikko' s redfish model : ))

[lentinj]

Thanks! Shall do.

g3a_initial_ageprop() will definitely be useful, I've seen it out-and-about before. Would it make sense to move the inversion inside the function though?

g3a_initial_ageprop <- function(alpha = g3_parameterized('mat_initial_alpha', by_stock = by_stock),
                                a50 = g3_parameterized('mat_initial_a50', by_stock = by_stock),
                                mature = FALSE,
                                by_stock = 'species'){
  out <- gadget3:::f_substitute(~bounded(-1 * alpha * (age - a50), 0, 1),
                         list(alpha = alpha,
                              a50 = a50)
  )

  ## Invert for immature stock
  if(!mature) {
    out <- gadget3:::f_substitute(quote( 1 - out ), list(out = out))
  }

  return(out)
}

What would be really nice is to be able to do something like (if (stock_hasnamepart(stock, "mat")) 1 else -1) * out, so you don't have to manually set mature on or off. I just made that up mind, but eminently do-able.