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CONTENTS
1. Introduction ................................................................................................................1
1.1. General Overview of the Program Coleraine....................................................... 1
1.2. General Overview of the Estimation Model ......................................................... 1
1.2.1. Abundance dynamics by sex......................................................................... 1
1.2.2. Initial conditions............................................................................................. 2
1.2.3. Stock–recruitment ......................................................................................... 3
1.2.4. Growth........................................................................................................... 4
1.2.5. Weight at age relationship............................................................................. 6
1.2.6. Selectivity ...................................................................................................... 6
1.3. Data ..................................................................................................................... 9
1.3.1. Predicted abundance indices ........................................................................ 9
1.3.2. Predicted age and size composition.............................................................. 9
1.4. Objective Function............................................................................................. 10
1.4.1. Robust normal likelihood for proportions:.................................................... 11
1.4.2. Abundance indices ...................................................................................... 11
1.4.3. Total likelihood ............................................................................................ 11
1.4.4. Penalties...................................................................................................... 12
1.4.5. Prior............................................................................................................. 12
1.4.6. Global objective function ............................................................................. 12
1.5. Policy evaluation................................................................................................ 12
2. Getting Started......................................................................................................... 14
2.1. Hardware Requirements.................................................................................... 14
2.2. Software Requirements ..................................................................................... 14
2.3. Outline of Working Environment........................................................................ 14
2.4. Necessary Files ................................................................................................. 14
2.5. File Management............................................................................................... 15
3. Getting Your Data into Coleraine ............................................................................. 16
3.1. General Issues .................................................................................................. 16
3.2. Default Values ................................................................................................... 16
3.3. Two Warnings.................................................................................................... 16