Add option in Build_Input_File to calculate time averages of catch, catch weight at age and selectivity at age by unique fleet

[michellesculley]

@JonBrodziak I'm updating the SS_to_AgePRO file to allow for these calculations. Currently, the total catch by fleet is calculated in the function to be the proportion of catch by fleet in the last year. Would you prefer the proportion of catch by fleet in each year or just output the catch by fleet in each year and do any additional manipulations in the Build_Input_File?

[JonBrodziak]

It would be preferable to output the catch by fleet in each year. Then set up the manipulations in the Build_Input_File, e.g. one default might be to output a 3-year weighted average.

On Wed, Jan 3, 2024 at 11:27 AM Michelle Sculley @.***> wrote:

@JonBrodziak https://github.com/JonBrodziak I'm updating the SS_to_AgePRO file to allow for these calculations. Currently, the total catch by fleet is calculated in the function to be the proportion of catch by fleet in the last year. Would you prefer the proportion of catch by fleet in each year or just output the catch by fleet in each year and do any additional manipulations in the Build_Input_File?

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[michellesculley]

I have tested the functionality of the SS_to_AgePro function for the annual models, it all seems to work properly. I have updated the 013_BuildAGEPROInputfile to allow for fishery selectivity at age, catch at age, and total catch to be calculated across a set of years. I also added the functionality to pull the F by fleet and average it across years to replicated F status quo type of projections. Some work is done for the quarterly time step, but I am still testing that code.

[JonBrodziak]

I am in the process of converting from the previous code used in Build_Input_File.R and its variants. Will probably have the changes made in a few days and will push these to the branch Meg made to handle the changes using version control. In general, it will be good to move towards using the branch feature to make future code changes and merge them into the main/origin branch.

[michellesculley]

I have tested both the Build_input_file and the 013_BuildAGEPROInput.R files and they seem to run well, produces an input file that runs in AGEPRO just fine. The issue with the Fishery selectivity at age inputs are fixed, and the calculation of the correct catch by proportion catch is fixed.