Virtual Population Analysis

FAO Fisheries Technical Paper 400

Virtual Population Analysis - A Practical Manual for Stock Assessment


Hans Lassen
and
Paul Medley

FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS

Rome, 2001

Table of Contents

The designations employed and the presentation of material in this publication do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries.

ISBN 92-5-104533-X

All rights reserved. Reproduction and dissemination of material in this information product for educational or other non-commercial purposes are authorized without any prior written permission from the copyright holders provided the source is fully acknowledged. Reproduction of material in this information product for resale or other commercial purposes is prohibited without written permission of the copyright holders. Applications for such permission should be addressed to the Chief, Publishing and Multimedia Service, Information Division, FAO, Viale delle Terme di Caracalla, 00100 Rome, Italy or by email to [email protected]

© FAO 2001

Download full ZIP file (799 kb)

TABLE OF CONTENTS

PREPARATION OF THIS DOCUMENTpdf

GLOSSARY AND ACRONYMSpdf

1 INTRODUCTIONpdf

1.1 OVERVIEW
1.2 BACKGROUND

2 OBJECTIVESpdf

3 WHEN TO USE VPApdf

4 THE POPULATION MODELpdf

4.1 THE COHORT MODEL
4.2 THE CATCH MODEL
4.3 COHORT PROJECTIONS
4.4 SEPARABLE VPA
4.5 POPE’S APPROXIMATION
4.6 CONVERGENCE BEHAVIOUR OF THE VPA PROCEDURE
4.7 SOLVING THE VPA EQUATIONS

4.7.1 Newton-Raphson Iteration
4.7.2 Functional Iteration
4.7.3 Least-Squares

4.8 MULTISPECIES VPA
4.9 COMPARISON WITH OTHER STOCK ASSESSMENT MODELS

5 LINK MODELSpdf

5.1 ABUNDANCE INDICES

5.1.1 Index Standardisation
5.1.2 Dis-aggregated Abundance Indices
5.1.3 Biomass Indices

5.2 FISHING MORTALITY INDICES
5.3 USING LENGTH COMPOSITIONS

5.3.1 Factors Affecting Length Frequencies
5.3.2 Length to Age Conversion

6 ERROR MODELS AND ESTIMATIONpdf

6.1 LIKELIHOOD
6.2 LEAST-SQUARES ESTIMATION

6.2.1 Weights

6.3 FINDING THE LEAST-SQUARES SOLUTION

6.3.1 Linear Models
6.3.2 Non-linear Models

6.4 ESTIMABLE PARAMETERS
6.5 ROBUST REGRESSION
6.6 CATCH

7 ASSESSING RELIABILITYpdf

7.1 SENSITIVITY ANALYSIS AND THE EFFECT OF HIGHLY INFLUENTIAL OBSERVATIONS
7.2 THE ANALYTICAL APPROACH TO VARIANCE-COVARIANCE ESTIMATION
7.3 ESTIMATING CONFIDENCE INTERVALS USING BOOTSTRAPS
7.4 ESTIMATION WHEN DATA ARE MISSING
7.5 RETROSPECTIVE ANALYSIS

8 ADAPTpdf

8.1 ADAPT WITH EXTERNAL WEIGHTING
8.2 SEVERAL ABUNDANCE INDICES
8.3 EXTENDED SURVIVOR ANALYSIS (XSA)
8.4 DOWN WEIGHTING OF OLDER DATA IN THE ANALYSIS
8.5 REGULARISATION

9 ASSESSMENT RESULTSpdf

9.1 PROJECTIONS OF FUTURE YIELDS AND STOCK DEVELOPMENT
9.2 SHORT TERM PROJECTIONS
9.3 STOCK RECRUITMENT

9.3.1 Fitting the Stock-Recruitment Curve

9.4 MEDIUM-TERM PROJECTIONS

9.4.1 Projection Methods

9.5 LONG-TERM CONSIDERATIONS

9.5.1 Biological reference points

9.6 FRAMEWORK FOR ADVICE

10 EXAMPLESpdf

10.1 INTRODUCTION
10.2 SINGLE COHORT

10.2.1 No Abundance Index
10.2.2 One Abundance Index
10.2.3 Uncertain Catch

10.3 MULTIPLE COHORTS

10.3.1 Separable VPA
10.3.2 Including Several Indices

10.4 STRUCTURED LINK MODELS
10.5 CROSSLINKED MODELS

10.5.1 Fitting the Model
10.5.2 Indicators and Reference Points

10.6 BOOTSTRAPPING BASED ON MONTE CARLO SIMULATIONS

10.6.1 Specifying Errors
10.6.2 Results

11 SPREADSHEETS WITH EXAMPLES AND EXERCISESpdf

12 REFERENCESpdf

CD ROM