Alaska Projection Scenarios for Stock Synthesis

Version: January 18, 2024

Created by Steve Barbeaux
E-mail: steve.barbeaux@noaa.gov
Phone: ‪(206) 526-4211‬

This function performs the 7 Alaska projection scenarios for Stock Synthesis 3 for tier 3 models. It runs the scenarios, saves them to the working directory, and produces stock figures for the projections. However, please note that this function could use some work on generalization and making the figures more suitable for assessment purposes.

Usage

In the starter.ss file, make sure to change it to read from the converged .par file: 1 # 0=use init values in control file; 1=use ss.par

Assumptions:

• You have already specified the forecast parameters appropriately in the forecast.ss file for scenario 1.
• There is no catch or F already specified in the forecast file.

Parameters:

• DIR: Model directory
• CYR: Model current year
• SYR: Start year for the model
• SEXES: Number of sexes in the model
• fleets: The fleet number/s in SS for your fisheries
• Scenario2: Indicates whether you wish to have a different catch for scenario 2 (1 = FmaxABC, 2 = F as S2_F, 3 = specified catch from a formatted CSV saved in the root directory named 'Scenario2_catch.csv', must have an entry for each year, season, and fleet for the years that differ from Fmaxabc with columns "Year, Seas, Fleet, Catch_or_F")
• s4_F is the F for scenario 4, defaults to 0.75, should be 0.65 for some species check your requirments
• do_fig: Whether to plot figures
• do_mark whether to make markdown tables
• URL is the url address of the previous stock assessment document
• pdf_tab is the table number in the pdf to collect executive summary table data
• init_dir is the director of the AK_SCENARIOS_FOR_SS files.

Output

SSB
This provides all output from the model start year to the final projection year as specified in the forecast file for each scenario. Table with columns Yr, TOT, SUMM, SSB, std, F, Catch, SSB_unfished, and model. Yr = year, TOT = total biomass, SUMM= Summary biomass as specified in the starter file, SSB is the female spawning biomass, std = standard deviation of the female spawning biomass, F = sum apical F, Catch = total catch, SSB_unfished = unfished female spawning biomass, and model = Scenario.

CATCH
This provides projected catch estimates for each scenario. Table with columns Yr, Catch, Catch_std, and model, Yr = year, Catch = total catch, Catch_std = standard deviation of the catch, and model = scenario.

Two_year
Table with projections out two years. Table with columns Yr, SSB, SSB_PER, SB100, SB40, SB35, F40, F35, C_ABC, C_OFL.

Tables
List with two three tables including Catch, F, and SSB corresponsing to the standard projection tables included in the stock assessment

FIGS
List with two sets of figures including standard projection figures showing spawning biomass and catch projections.

Example figures:
SSB

Catch

Example usage:

profiles <- Do_AK_TIER_3_Scenarios(DIR = "Model_23.1.0.d", CYR = 2023, SYR = 1977,  SEXES = 1, FLEETS = 1, Scenario2 = 1, S2_F = 0.4,
					s4_F = 0.75, do_fig = TRUE, do_mark=TRUE,URL="https://apps-afsc.fisheries.noaa.gov/Plan_Team/2022/EBSpcod.pdf",
					pdf_tab=1, init_dir=" C:/Users/steve.barbeaux/Work/GitHub/AK_Scenarios_For_SS")