R. M. Sibly et al.
Population Regulation

Click here to download the following paper (free):

Sibly, R.M., Barker, D., Denham, M., Hone, J. and Pagel, P., 2005. On the regulation of populations of mammals, birds, fish and insects. Science 309: 607-610.

Associated software to investigate population regulation follows.


Introduction
Citing the software
Download software
Instructions for use
Adapting the software to run under R
Credits

Introduction

A free computer program for estimating theta in the theta-logistic (or generalized logistic) population model may be downloaded here. The program was written by Daniel Barker and Mike Denham. The program is an S-Plus script and requires Insightful S-Plus for Microsoft Windows. (If using R instead of S-Plus, please see Adapting the software to run under R.)

The generalized logistic equation is:

pgr = r0[1-(N/K)theta],

where pgr is the population growth rate, N is the population size, K is the carrying capacity, r0 represents pgr at N = 0, and theta describes the curvature of the relationship.

The program is based on software used in a recent large analysis of the GPDD database by Sibly et al. (2005). The program here is separate from the GPDD, however, and will estimate theta for one or more population time series provided by the user.

Citing the software

Please cite the paper if you use the program:

Sibly, R.M., Barker, D., Denham, M., Hone, J. and Pagel, P., 2005. On the regulation of populations of mammals, birds, fish and insects. Science 309: 607-610. Download (free)

Download software

Instructions for use

Instructions are given in a long comment at the start of the genlogistic.ssc script.

If you have downloaded the script, and have installed S-Plus for Windows, double-click the genlogistic.ssc file on your computer. You can then read the instructions in the script. When the input file is ready, as described in the instructions, choose Run from the S-Plus Script menu.

You may wish to run an analysis of the example genlogistic_in.xls file first, or use this as a template for your own input file. It contains made-up data, just intended to demonstrate the correct format.

Adapting the software to run under R

The genlogistic.ssc script was developed and tested under Insightful S-Plus. However, with slight adaptation it should be possible to make it work under the free R software environment, instead.

We have not attempted this ourselves, but here is useful advice from a user of the script, Simon Chamaillé-Jammes of the Centre d'Etudes Biologiques de Chizé - CNRS. "From my own experience the S-plus functions provided here are fully functional under R. The only changes that have to be made are to the data import/export functions in the section '# Main Program'. Replace guiImportData() and guiExportData() with your prefered way of loading and saving data under R, such as read.delim(), load(), etc. See the R documentation for more information. Note, this does not imply that there is no uncessary code or other ways of re-writing it under R. This advice is provided only for your personal information and cannot be considered a guarantee."

Support

Please send questions and bug reports to Daniel Barker.

Credits

This sofware was written by Dr Daniel Barker who was then at the University of Reading School of Animal and Microbial Sciences but now works at the University of St Andrews School of Biology, and Dr Mike Denham who was then at the University of Reading School of Applied Statistics but now works at GlaxoSmithKline. This Web site was developed by Dr Daniel Barker.

The software was developed as part of a NERC Small Research Grant to Professor Richard Sibly (Principal Investigator) and Professor Mark Pagel (Co-Investigator) at the University of Reading School of Animal and Microbial Sciences.


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