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Stock Synthesis 3

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Stock Synthesis (SS)


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Core Application

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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 in the population 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.  Some SS features include ageing error, growth estimation, spawner-recruitment relationship, movement between areas.  SS is most flexible in its ability to utilize a wide diversity of age, size, and aggregate data from fisheries and surveys.  The ADMB C++ software in which SS is written searches for the set of parameter values that maximize the goodness-of-fit, then calculates the variance of these parameters using inverse Hessian and MCMC methods.  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, including forecasts of possible annual catch limits.  The structure of Stock Synthesis allows for building of simple to complex models depending upon the data available.


The GUI interface for Stock Synthesis uses the Microsoft .Net framework and supports enhanced features such as screen resizing.  The GUI supports all core features of SS, except some specialized features, particularly tag-recapture and generalized size frequency data.   At this time, the GUI is compatible with an older version of SS input/output file format, so this older SS executable is bundled with the GUI download, and the newest SS executable for various operating systems, with documentation, helper spreadsheets, and examples, is provided as a separate download.

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Download Stock Synthesis Version 3 Now

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Version History


SS3 Text Version 3.23b (Nov 8, 2011) w/calculation engine 3.23b

SS version 3.23b provides a roll-up of various augmentations to the output files and introduces new growth and super-period features.  Consult the SS-Change-log.xlsx for searchable list of all updates.


SS3 Text Version 3.21d  (June 2, 2011)   w/calculation engine 3.21d

SS version 3.21d provides some corrections to the forecast module, introduces cubic spline selectivity options, and introduces a survival basedspawner-recruitment relationship.

SS3 Text Version 3.21a  (April 26, 2011)   w/calculation engine 3.21a

Version 3.21a of SS contains multiple fixes and new program features.  Please refer to the change log in the documentation download for full details.

SS3 Text Version 3.20b  (January 26, 2011)   w/calculation engine 3.20b

Version 3.20 of SS introduces several new capabilities:  enhanced forecast module, 3 parameter spawner-recruitment functions, ageing error as parameters, reporting of a true annual F.  Some of these changes have mandatory changes to the input files, so review the documentation provided.

SS3 Text Version 3.11c  (November 2, 2010)   w/calculation engine 3.11c

SS version 3.11c contains corrections to the reporting of fishery body weight in models with time-varying growth or multiple seasons.  See the change log for more details and some minor augmentations.  The next release will contain:  ability to estimate ageing precision as parameters, 3-parameter spawner-recruitment functions, and enhanced capability for the "super-year" approach.

SS3 Linux Versions 3.11b  (October 14, 2010)   Linux versions of 3.11b

SS3 Text Version 3.11b  (September 24, 2010)   w/calculation engine 3.11b

Version 3.11b of Stock Synthesis corrects problem with a seasonal model.

SS3 Text Version 3.11a  (September 23, 2010)   w/calculation engine 3.11a

Version 3.11a of Stock Synthesis principally addresses several minor revisions accumulated since the last major release in early 2010. These are documented in the file SS_Change_Log.xlsx,  which replaces the Change Log section of the User Manual. In addition, there has been a major re-working of the time-varying growth section to achieve better performance. Users of time-varying growth should upgrade and should expect small changes in results. There are no mandatory input changes with this version. Some changes in output have occurred and are being worked into the R4SS output processor.

SS3 GUI Version 3.1.0 (March 8, 2010)   Updated to support calculation engine 3.10b

SS3 Text Version 3.10b  (March 1, 2010)   w/calculation engine 3.10b

Version 3.10b corrects a problem that occurred in some multi-season model configurations.

SS3 Text Version 3.10a  (February 23, 2010)   w/calculation engine 3.10a

SS3 Text Version 3.10  (February 22, 2010)   w/calculation engine 3.10

Version 3.10 of Stock Synthesis principally addresses augmentations to the empirical body weight-at-age input ( and enhancements to the non-parameteric age selectivity (pattern #17).  All users should read over the change log near bottom of the User Manual for a list of all fixes and changes.

SS3 Text Version 3.04b  (October, 8, 2009)   w/calculation engine 3.04b

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

SS3 Text Version 3.04a  (September 15, 2009)   w/calculation engine 3.04a

Version 3.04a fixes a few output problems with 3.04.

SS3 Text Version 3.04  (September 9, 2009)   w/calculation engine 3.04

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

SS3 Text Version 3.03a (May 12, 2009)   w/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)

SS3 Text Version 3.02b (January 2009)

SS3 Text Version 3.01o (December 2008) 

SS3 Text Version 3.01h (September 2008) 


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Older Version Changes 


First release of version 3 was 3.01h


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NOAA Fisheries Toolbox Version 3.1

website last modified May 16, 2016


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