2023 Stock Synthesis Models

List all SS models (and their associated information) in the table below:

Model designation	Date Run	Branch/Fork	Status	Assigned	Major Changes/Notes	Model name
2013 v3.24	02/12/23	B: 2013_ss_model	Merged (02/14/23)	JZ	Reproduces 2013 assessment results using 2013 SS version.	12.sq
2013 v3.30 bridge	02/24/23	B: 2013_bridge	Merged (02/24/23)	JZ, MV	Reproduces 2013 results using modern SS version.	23.sq.fixQ
2023 base model		B: 2023_ss_base	In progress		2013 model structure but using updated data through 2023

Major implementations in the SS input files to transition the 2013 model from SS v3.24 to SS v3.30

name of the corresponding variable in the control file are specified as (variable_name)

Control file

1- Recruitment settlement assignements

(recr_dist_pattern)

SS V3.30 needs the timing and age of settlement to be specified. According to the Stock Assessment of Shortspine Thornyhead in 2013: * Shortspine thornyheads along the West Coast spawn pelagic, gelatinous masses between December and May (Wakefield, 1990; Erickson and Pikitch, 1993; Pearson and Gunderson, 2003) * Juveniles settle at around 1 year of age Consequently, the calendar age of settlement has been set equal to 1 and month of settlement equal to 3 in order to mimic end February (timing between December and May).

2- Blocks and time varying parameters

Controls for TV parameters (time_vary_adjust_method) needs to be checked. The Deviation adjust method used in SS3.24 ( from previous SS3 versions (e.g., SS3 v.3.24) is no longer an option.) is no longer an option. Here ther it has been set with no bound check. Maybe needs to be turn to 1 with warning relative to base parameter bounds. See (DoAdjust) & (selex_adjust_method) for selectivity TV param

3- Biology and other long line parameters

WARNING: Different names and order of the columns: the order of PRIOR SD and PRIOR TYPE have been switched and the PRIOR TYPE options have been renumbered. Also need to change the row ordering to fit females; males and then recruitment distribution,...

4- Equilibrium Recruitment

Steepness is not used in the computation of the initial equilibrium recruitment because that option was not available in previous versions of SS. This might be changed?

5- Catchability

Catchability parameters matrix for SS V3.30 is really different from the one used in V3.24. => In the 2013 model:

• Each fleet was directly proportional to abundance,
• There was no environmental impact on Q,
• Only the Triennial1 survey had an extra parameter that will contain an additive constant to be added to the input stddev of the survey variability,
• Each fleet has a Q set as a scaling factor such that the estimate is median unbiased <=> Q "float"

=> For this transition and as a first step:

• Each fleet has a simple Q, directly proportional to abundance (i.e., link = 1)
• the Extra input for link information is set to 0 to mimic the default option of previous version of SS
• An extra standard error is estimated for the Triennial1 survey. The estimate from the 2013 model is used as input to set up this parameter See the additional parameter line in the Q_parms matrix
• We don't incorporate priors at this stage so no bias adjustement are applied (i.e., biasadj = 0)
• Q is fixed, i.e., by no floating (float = 0) and not estimating (PHASE = -1)

forecast file

1- Forecast selectivity Set as the mean from year range