GARP Modelling System User’s Guide and Technical Reference

The following manual has been moved from its original location.

by Karen Payne and D.R.B. Stockwell

Introduction

Welcome to the GARP Modelling System (GMS)! GARP is an acronym for Genetic Algorithm for Rule Set Production. The GMS is a set of modules primarily designed for predicting the potential distribution of biological entities from raster based environmental and biological data. The modules perform a variety of analytical functions in an automated way, thus making possible rapid unsupervised production of animal and plant distributions. This manual describes the use of the software which has widespread application where a simple to use, robust and informative modelling system is needed.

The package you have just downloaded consists of three parts. First, this manual which is intended to serve as a gentle introduction to those interested in using the GMS. Secondly, you have all the programs necessary for using the GMS. Finally, this package also contains a small example data set and scripts for running them, do.x and do2.x. These examples are referred to in this tutorial paper.

• Introduction
• Administrative matters

• copyright
• caveat
• revision history
• retreiving and installing garp
• contacting the author
• other sources of information
• conventions used in this manual
• a note on the examples provided
• general structure of analytical systems
• general structure of this manual

• The database

• parameters
• rasteriz
• presampl

• The modelling tools

• initial
• overview of logic and probability
• rule types
• explain
• introduction to genetic algorithms
• predict
• verify

• Visualisation

• image

• Acknowledgements
• References
• Man pages
• Links

Administrative matters

Copyright

This program is the copyrighted and intellectual property of David Stockwell. Permission is given to use this program for evaluation. For regular use a fee may be charged.

Caveat on the use of the GARP modelling package

The author disclaims any warranties of fitness of programs for any particular problem.

Revision history

This is version 1.0, the first public release version of GARP.

Downloading and installing the GMS

GARP is available for download from biodi.sdsc.edu

Installation

This package is a C coded version of an earlier system called Ttree which was written in Turbo PROLOG for MSDOS. This version has run successfully on Sun workstations and IBM PC’s (using Linux).

Installation in UNIX

The following commands should compile the programs. Modify the makefile for system specific compilers and installation destination.

Unzip, untar and compile.

  > gunzip garp-1.0.tar.gz
  > tar xovf garp1.0.tar
  > make all

Installation in DOS

For DOS installation use the syntax:

  >pkunzip -d garp_1.0.zip

in your garp directory.

After you install garp you should have on your system the following files on your system:

• executables

rasteriz*
initial*  
presampl*
explain*
predict*
verify* 
image* 
translat*

• documents

CAVEATS 
COPYRIGHT 
FAQ 
README
garp.txt
formats.txt
rasterize.txt
initial.txt
presample.txt
explain.txt
predict.txt
verify.txt 
image.txt 
translate.txt 
index.txt

• batch files

mod.x*
multi.x*

• data

Example/ 
Example2/

Contacting the author

Bugs, comments, money, contracts and general praise of the GMS can be directed to the author via one of the following contacts:

David Stockwell

davids99us at yahoo.com

What published information and applications are available?

Biodi also has supporting documentation in addition to links to other relevant sites and can be viewed at: http://biodi.sdsc.edu.

You may also wish to joint the GARP public mailing list by sending the message:

> subscribe garp 

to

majordomo@sdsc.edu

The list owner is David Stockwell and can be contacted at either of the following email addresses: davids@sdsc.edu

If you are interested in learing more about genetic algorithms you may view the Genetic Algorithms FAQ from the newsgroup comp.ai.genetic.

A note about the notation used in this manual

File names are given in quotation marks (eg. "test"). Commands that you would type in at your terminal are preceeded with a > indicating the machine prompt. cd means change directory.

A note on the examples provided

Example programs are included for testing and tutorial. These are contained in the directories Example and Example2. To run the GMS on these examples on UNIX or DOS machines cd to the "Example" directory and type:

  > do

This example uses most of the model development tools in their typical usage. The output is an ascii map of a 20×20 distribution of Greater Glider density. To run the second example cd into "Example2" and type:

  > do2

This example applies the rules developed in "do" to a 140×100 map to predict the density of Greater Glider over a larger area. The output are images in portable grey map (pgm) format. You will need an image viewer such as xv to view or convert these images.

It may be useful to examine the files "do", "do2" and "parameters" as an example of how to run GARP in a batch mode. A typical batch file for a UNIX machine, the "do" file, is shown below:

set -x
echo "Datadir Example" > paramete
cp Example/layer00 .
./presampl -prop
./initial
./explain
cat test | ./verify
./predict | ./image -pnm
./translat
cat predI.pgm

Each line of the batch file is a separate command to the operating system which is executed in order in the batch file. The pipe symbol (|) directs the output of one program into the input of another. The redirect symbol (>) directs the output of one