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PIFSCstockassessments / 2024-WCNPO-MLS-Rebuilding

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Update MLS female maturation probabilities at age to match spawning season-aged fish #15

Closed JonBrodziak closed 7 months ago

JonBrodziak commented 7 months ago

Currently the MLS female maturity-at-age probabilities are output from 013_BuildAGEPROinputfile.R and Build_Input_File.R and its variants as occurring at the beginning of the year (January 1st) for ages Year-0.5 ages. These maturation values need to be output for the spawning season (July 1st) for ages Year+0 ages. That is, the current maturity values underestimate the predicted values from the maturity ogive. Probabilities for age-0, age-1, age-2 female MLS are 0.0033, 0.2171, and 0.8934 on July 1st for checking. I have been manually adjusting the maturation probabilities in the Agepro input files but it would be best to automate this.

michellesculley commented 7 months ago

I have adjusted the maturity at age computation in the SS_to_AGEPRO.R file to use the size at age in quarter 3 instead of quarter 1. These should now reflect the fish on their birthdays, starting age 1.