Cstar Version 1.1

by Athol Whitten, March 2014

The Project

The Cstar (Common Stock Assessment Routines) project aims to collect, collate, and document common fisheries stock assessment modeling routines and to make them available as an open-source function library for ADMB (Auto-differentiation Model Builder). ADMB is a powerful software package for the development of nonlinear models and is freely available from the ADMB-project website.

The library should simplify the development of fisheries stock assessment models and fish population models of all varieties. Development will be focussed on commonly used size-based functions for the assessment of hard-to-age species. For more information, please contact Athol Whitten at the School of Aquatic and Fishery Sciences, University of Washington.

The Cstar library can be used for building new stock-specific population and assessment models, or for simplifying existing ones. As an example, Cstar functions have been used, in part, to build a Generalized Model for Alaskan Crab Stocks (Gmacs). More information on Gmacs can be found at its Github repository. The Gmacs source code includes calls to pre-existing functions from the Cstar library, eliminating the need for the main code to contain extra lines that define commonly used functions.

Collaborators

Interested persons can collaborate on this open-source project by contacting Athol Whitten. Collaborators may work on their own branch of the Cstar repository and make a pull request when comitting changes to the code. Some collaboators may wish to provide their Github username and be given read-write access to the repository.

Cstar Coding Standards

1. Assume all base types are double

2. Use Google style guide: http://google-styleguide.googlecode.com/svn/trunk/cppguide.xml

Users

The entire Cstar repository can be downloaded to a local machine by clicking the Download Zip button on the main repository page. Github users can clone the repository using their preferred method.

Instructions for use:

• Download the Cstar repository and save it to your local machine.

• Copy the Cstar folder to a directory that is in your PATH or can be referred to in your ADMB code, and use the #include<cstar.h> pre processor command in the GLOBALS_SECTION of your TPL file.

• Cstar functions should now work from directly within your model code.

ToDo List

• Sort out namespace issues for cstar (3 letter namespace -> car)
• Remove the #includes ".cpp" in header file cstar.h
• Clean up bugs in approx.
• Remove selex class in cstar.h, now using selex.hpp template.
• Doxyfile for doxygen comments.
• Work on template libraries for log density functions
• Add alternative selectivity functions to selex.hpp
• Create shared object library for cstar
• Create makefile for building shared object library
  • Unix makefile
  • Windows makefile