Stock Synthesis
Version 3 is the follow-on to SS2.
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.
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.
