Stock Synthesis 3

Stock Synthesis provides a statistical framework for calibration of a population dynamics model using a diversity of fishery and survey data. It is designed to accommodate both age and size structure and with multiple stock sub-areas. Selectivity can be cast as age specific only, size-specific in the observations only, or size-specific with the ability to capture the major effect of size-specific survivorship. The overall model contains subcomponents which simulate the population dynamics of the stock and fisheries, derive the expected values for the various observed data, and quantify the magnitude of difference between observed and expected data. Parameters are searched for which will maximize the goodness-of-fit. A management layer is also included in the model allowing uncertainty in estimated parameters to be propagated to the management quantities, thus facilitating a description of the risk of various possible management scenarios. The structure of Stock Synthesis allows for building of simple to complex models depending upon the data available.

The GUI interface for Stock Synthesis has been completely rewritten for version 3 to use the Microsoft .Net framework and to support enhanced features such as screen resizing, however the GUI version does not support all features of the program. These features, particularly tag-recapture and generalized size frequency, are fully described in the user manual and can be invoked by editing the input files using a text editor. The same executable program, SS3.exe, is used in association with the GUI or directly with text files.

The evolution from SS2 to SS V-3 was motivated by several factors. The experience gained from use of SS2 led to the identification of several model features needing fuller control and more options. The use of SS for more situations with precise catch-at-age data and high levels of fishing mortality also expanded the range of needed options. The possibility of using SS for more tuna assessments led to the need for better control of seasonally varying parameters, addition of weight frequency data, better control of movement parameters, and capability to include tag-recapture data. A fundamental internal change is the separation of the population length bin structure from the length data bin structure. This was necessary to create the new generalized size frequency capability. Now selectivity, weight-at-age, and other properties can be calculated more precisely from finer grained population length bins, while existing length data bins can remain unchanged.

V3.04b fixes a few output problems, especially for single gender configurations, and adds optional features as documented in the version log.

Version 3.04 of SS represents an accumulation of changes since the release of SS V3.03 in early 2009.

The User Manual contains a section titled "Version Log" which outlines the various code fixes, clarifications and new features.

Notable new features include hermaphroditism, input of empirical body weight-at-age, more control of the mean-median bias offset for recruitments, rewriting the Excel output processor for Office 2007, fishing effort as a "survey" of F, more time-varying parameter options, and others.

SS3 GUI Version 3.0.14 (May 29, 2009) Updated to support calculation engine 3.03a

The version log portion of the updated User Manual describes these changes in full, including 2 mandatory additions to the input control file.
In particular, this new version includes:
    Several more options for time-varying parameters (including non-linear trends and additive devs)
    A rudimentary hermaphroditism option
    More control on the level of recruitment bias adjustment
    Expanded output of derived management quantities
    New Excel 2007 output processor

SS3 GUI Version 3.0.13 (April 8, 2009) w/calculation engine 3.02E, no changes to GUI

SS3 GUI Version 3.0.12 (February 5, 2009) w/calculation engine 3.02D with corrections to the reporting of mean body size-at-age in models that use multiple seasons or sub-morphs.

SS3 GUI Version 3.0.11 (January 2009) (First non-beta GUI release, calc engine 3.02c)

First release of version 3 was 3.01h

NOAA Fisheries Toolbox Version 3.1

website last modified November 13, 2009

GUI Version 3.0.14/3.03a (May 2009)	Core Application
Text Version 3.04b (October 2009)

Stock Synthesis Version 3 (SS3)

Stock Synthesis Version 3
(SS3)