Fisheries No. 8

stock assessment tools II
User’s guide

prepared by
F.C. Gayanilo, Jr
National Center for Caribbean Coral Reef Research, University of Miami
Miami, United States of America
P. Sparre
Danish Institute for Fisheries and Marine Research
Charlottenlund, Denmark
D. Pauly
Fisheries Centre, University of British Columbia
Vancouver, Canada


Rome, 2005

Table of Contents

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ISBN 92-5-105300-6

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

© FAO 2006

Gayanilo, F.C.Jr.; Sparre, P.; Pauly, D.
FAO-ICLARM Stock Assessment Tools II (FiSAT II). Revised
version. User's guide.
FAO Computerized Information Series (Fisheries). No. 8,
Revised version. Rome, FAO. 2005. 168 p.
(Includes a CD-ROM with the software)


FiSAT II is a program package consisting of methodologies for use with computers, enabling users to formulate some management options for fisheries, especially in data-sparse, tropical contexts.

The FiSAT II was developed for computers running on Microsoft Windows operating systems. The new version utilizes the standard Windows graphic user interface.

FiSAT II was developed mainly for the analysis of lengthfrequency data, but also enables related analyses, of size-atage, catch-at-age, selection and others.

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Fisheries No. 8pdf

Preparation of this document

Chapter 1. Getting started

What you will learn from this chapter
About the package
System requirements
Installing and starting FiSAT II
The graphic user interface

The main user interface
User inputs to FiSAT II
Using the menu bar

Chapter 2. HELP facilities

What you will learn from this chapter
Types of HELP messages
Accessing HELP
On-line help messages
FiSAT II on the web
Technical support

Chapter 3. FILE menu

What you will learn from this chapter
Types of files
Time series of length frequencies
Length frequencies grouped by constant class size
Ungrouped length frequencies
Data grouped by variable class sizes
Growth increments
Catch in numbers by age
Series of mean lengths and standard deviations
Probabilities of capture
Table of values
Two-column regression files
Species table
Fleet table
Multispecies/multifleet scenario

Creating a file
Printing a file
Sample manipulation
Merging two files
Correcting using probabilities of capture
Adjusting class intervals
Smoothing data files
Pooling samples
Converting files
Raising samples
Using catch per unit of effort (C/f)
Using catch/sample weight
Using a constant
Percent of sample total
Square root of sample total
Temporal weighting
Importing old FiSAT data
Exporting FiSAT II length frequencies

Chapter 4. ASSESS menu

What you will learn from this chapter
The format in module description
Parameter estimation
Direct fit of length-frequency data
Shepherd's method
Powell-Wetherall plot
Analysis of length-at-age data
Modal progression analysis
Bhattacharya's method
Linking of means
Analysis of growth increment data
Gulland and Holt plot
Munro's method
Fabens' method
Appeldoorn's method
Mortality estimation
Z from steady-state sample
Length-converted catch curves
Jones/van Zalinge plot
Z from mean length
Beverton and Holt model
Ault and Ehrhardt method
Hoenig's model
Natural mortality
Rikhter and Efanov's method
Pauly's M equation
Recruitment patterns
Probabilities of capture
Trawl-type selection
Gillnet selection
Virtual population analysis
Age-structured VPA
Length-structured VPA
Relative Y/R and B/R analysis:
Knife-edge selection
Using selection ogive
Thompson and Bell yield and stock prediction

Chapter 5. SUPPORT menu

What you will learn from this chapter
Simulation of length-frequency samples
Sample weight estimation
VBGF and L/F plot
Maximum length estimation
Growth performance indices
Regression analysis


A. Terms and variables
B. References