This is the pilot release of Gmacs. Currently posted source files are compilable using ADMB 11.1 and have been tested using the BBRKC model available in the examples folder. This release will remain active until the current 'under development' version is released. Updated February 2014, by Athol Whitten
This repository holds source code, instructions, examples, and associated scripts for Gmacs (Generalized Modeling for Alaskan Crab Stocks), a generic size-based stock assessment model.
Gmacs implements a size-structured modelling framework with flexibility similar to that provided by other general stock assessment modelling frameworks. Some effort has been made to maintain consistency with data and control file formats familiar to users of Stock Synthesis.
Data are supplied via the model.dat file in a flat format to enable easy indexing and simple preparation using spreadsheet software. Each record for catch, abundance, length-structure etc. should be held in an individual row, with information relating to year, fleet, sex and more:
- Year, Season, Fleet, Sex, Observation
- Year, Season, Survey, Observation, Error
- Year, Season, Fleet/Survey, Sex, Maturity, Shell Condition, No. Samples, Data
Gmacs allows for the inclusion of an optional growth data file growth.dat to specify a fixed growth transtion matrix or year-specific growth transtion matrices. The program also reads a starter.gm file for specifying the overall model run conditions, and a control file model.ctl for specifications relating to parameter estimation. Finally, a forecast.gm file is read to specify the calculation of relevant reference points. This file will allow users to specify model projection options in later versions of Gmacs.
During the read-in procedure, helpful messages are printed to screen and the information read in is printed to a separate file called echoinput.gm allowing users to check and debug their data and control files.
A general user-guide to the program is under development and will be made available with future releases.
This software is under development and is not yet intended for general use. If you would like to contribute to the project, please contact Athol Whitten.