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Examples of Different Implementations of Catch at Age Models

The purpose of this page is to serve as a shared repository for ADModel Builder™ code used for analyses of fishery data.

DISCLAIMER: These models are intended to provide example applications only. They do not represent complete models used for stock assessment and fishery evaluations by any management body.

  • A Ricker stock-recruitment curve fit with explicit errors in stock size. This is a very simple example of how errors-in-variables type problems can be addressed. Click here for the template and datafiles.

  • Simple catch-at-age using flack lake trout data (from Hilborn and Walters). This model is one example that ships with ADModel Builder. A zipped up version can be found here.

  • An age structured model for Gulf of Alaska sablefish. This example model is of the aggregate population (sexes combined) but is tuned to sex-specific length frequency data. This has examples of ways to bin different age groups and demonstrates how modeled age classes can be processed to fit observed length frequency data. The template and datafiles can be viewed here.

  • Schnute and Richards (1995) CJAFS model is implemented in this example applied to Pacific ocean perch. Here, the model formulations drawn up are directly from their paper but the objective function was modified slightly to avoid problems age classes that had no observations. Note the use of "posfun()" to avoid having the stock attain negative values during the non-linear search routine. The template, pin(parameter input file), and the data files. These files were kindly provided by Laura Richards, DFO, Canada. An alternative form for this model (using Baranov's catch equation can be seen here with data file here.

  • Age structured model for eastern Bering Sea yellowfin sole. This application (template file) is tuned to a single survey (for which catchability is estimated). The organization of the datafile follows the convention of using calendar years for valid indices of observation arrays. This makes using data with missing years easier.

  • Age structured model used for evaluating the NRC's (National Research Council's) Expert Panel on Fisheries Stock Assessment datasets. This model represents a fairly comprehensive treatment of fishery and survey data where a wide variety of processes are modeled. For example, survey AND fishery catchability are allowed to change over time and effort was assumed to be measured with error. During the last phases of minimization a robust objective function. The write-up of this model can be found in zipped-postscript (260k) form here The template file can be viewed here with one of the NRC data files shown here. This code makes extensive use of what I have called control flags. These serve a variety of purposes from specifying prior variances to certain processes to performing retrospective analyses.



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