Forecast File Inputs not copying?

[Mkrig24]

I am running an MSE using sablefish stock assessment files, which have catch inputs specified at the bottom of the forecast file that cap catch at the ACLs set by council in the first two years of the model. When the model runs outside of SSMSE these inputs correctly cap the catch, but I noticed that inside of run_SSMSE, when the forecast file gets copied to _EM_init these input values aren't copied over, and the catch ends up being significantly higher.

becomes

Is there a way to make sure these inputs are copied over? Or another work around to get catch specified correctly in these first two years?

[k-doering-NOAA]

@Mkrig24 thank you for the question! Here is the code that is removing the forecast catch inputs:

SSMSE/R/manipulate_EM.R

Lines 395 to 402 in 1f12b27

	# get rid of Forecatch, if any. Add a warning to the user about this.
	# may beed to treat this differently in the futured
	# TODO: Implementing lag in assessment data (i.e. I run an 2020 assessment with
	# only data to 2018 and providing management advice for 2021) will require the
	# use of the ForeCatch input as well as a method to update what values to input.
	if (!is.null(fore[["ForeCatch"]])) {
	warning("Removing ForeCatch from the EM forecasting file.")
	fore[["ForeCatch"]] <- NULL

This was done because there isn't one obvious way to apply forecast catch inputs as the simulation projects forward in time without the user providing additional information.

Right now, I believe the only way to get catch specified in the forecast file would be to develop a custom management procedure - @nathanvaughan-NOAA, does that sound correct?

[nathanvaughan-NOAA]

That is all correct @k-doering-NOAA we have similar issues in the Southeast with a lag between the assessment data end year and management implementation year but don't have a good solution at the moment for defaulting this setup in SSMSE. A custom management procedure is likely the only solution if you want to explicitly include this in an MSE. @Mkrig24 if you look at the merge_catch_bias branch we are currently working on developing some custom EM's in the ratioBiasEM.R file that may help you with figuring out how to setup your own custom EM.