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Stock Synthesis User Manual : Version 3.30.15
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  • Alternative Title:
    Stock Synthesis User Manual Version 3.30.15
  • Description:
    Stock Synthesis (SS) is an age- and size-structured assessment model in the class of models termed integrated analysis models. SS has a population sub-model that simulates a stock’s growth, maturity, fecundity, recruitment, movement, and mortality processes, an observation sub-model estimates expected values for various types of data, a statistical sub-model characterizes the data’s goodness of fit and obtains best-fitting parameters with associated variance, and a forecast sub-model projects needed management quantities. SS outputs the quantities, with confidence intervals, needed to implement risk-averse fishery control rules. The model is coded in C++ with parameter estimation enabled by automatic differentiation (admb). Windows, Linux, and iOS versions are available. Output processing and associated tools are in R, and a graphical interface is in QT. SS is available from NOAA’s VLAB. The rich feature set in SS allows it to be configured for a wide range of situations. SS has become the basis for a large fraction of U.S. assessments and many other assessments around the world. This manual provides a guide for using SS. The guide contains a description of the input and output files and usage instructions. An overview and technical description of the model itself is in Methot and Wetzel (2013). However, SS has continued to evolve and grow since the publication in 2013, with this manual reflecting the most up to date information regarding SS. The model and a graphical user interface are available from the NOAA VLAB. The VLAB site also provides a user forum for posting questions and for accessing various additional materials. An output processor package, r4ss, in R is available for download from CRAN or GitHub.
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