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Extended Simple Stock Synthesis

Extended Simple Stock Synthesis (XSSS) is an assessment method for application to data-limited stocks. XSSS uses adaptive importance sampling to update parameter priors based upon index data.

Code available on this website comes with no warranty or guarantee of accuracy.

Installation

install.packages(c("devtools", "kableExtra"))
library(devtools)

devtools::install_github("CWetzel/XSSS", build_vignettes = TRUE)

Note: devtools may give this message: "WARNING: Rtools is required to build R packages, but is not currently installed." However, Rtools is NOT required for installing xsss via devtools, so ignore the warning.

Once you have installed the xsss package, it can be loaded using:

library(xsss)

A vignette is available and can be accessed with

vignette("xsss")

Setting up a model

XSSS is data-limited assessment approach for application when only catches and indices of abundance are available allowing for multiple fishing and survey fleets. XSSS requires four input files used by Stock Synthesis: starter, forecast, data, and control file. Biological relationships (e.g., weight-at-length, fecundity, maturity) and selectivity forms must be defined in the control file. Example model files are located within the "example" folder.

Running XSSS

The user must define distributions for three parameters: natural mortality, steepness, and relative stock status is a specific year. Example model files and calls to the main function are included in the "example" folder. Please see the vignette for additional information.

Software requirements

XSSS is written to work with Stock Synthesis version 3.30.11 or later. The latest version of Stock Synthesis and user manual is available on NOAA Vlab. A user account may be created for non-NOAA indivuals by contacting chantel.wetzel@noaa.gov. An executable for Stock Synthesis version 3.30.11 is included in the "examples" folder.

Description of package

Wetzel, C.R., and Punt, A.E. 2015. Evaluating the performance of data-moderate and catch-only assessment methods for U.S. west coast groundfish. Fisheries Research, 171: 170-187. https://www.sciencedirect.com/science/article/pii/S016578361500185X