Software
Software Developed by
Department of Fishery and Wildlife Biology and
Colorado Coop. Fish and Wildlife Unit,
Colorado State University
Most of the files provided on this page require pkunzip to unzip them.
One of the problems with obtaining software from the Web is that hard copy documentation is not available, such as is the case for Program MARK. The following sites provide information on how to cite electronic documents: MLA-Style Citations of Electronic Sources and Electronic Sources: APA Style of Citation .
Program MARK
Program MARK is a new software package currently being developed. A Windows 95, 98, NT, 2000, XP, or 7 program, Program MARK provides parameter estimates from marked animals when they are re-encountered at a later time. Re-encounters can be from dead recoveries (e.g., the animal is harvested), live recaptures (e.g. the animal is re-trapped or re-sighted), radio tracking, or from some combination of these sources of re-encounters. Check out the description of its capabilities, or information on how to download the program.
BROWNIE
BROWNIE computes survival estimates from banding (ringing) recovery data from young and adult animals. The methods and user’s manual are documented in:
The source code, executable for DOS, and example input files are included in the zip file. The models computed with this code can now be done with Program MARK, and continued use of BROWNIE is not recommended. For further information, contact Gary White.
CAPTURE
CAPTURE computes tests to select a model from 11 possible models, and then the population estimate for capture-recapture data on closed populations. The methods are documented in:
The latter document contains a user’s manual (Appendix A) and numerous examples for CAPTURE. An interactive interface (2CAPTURE) is available from Dr. Kenneth Burnham at the same address (and includes its own 2CAPTURE manual), or via email to kenb@lamar.colostate.edu. Unix (SUN), Microsoft FORTRAN for PC’s, and Ryan-McFarland FORTRAN for PC’s source code for CAPTURE is stored in the subdirectories pub/capture/unix-src,pub/capture/ms-src, and pub/capture/rm-src available via anonymous ftp to ftp.cnr.colostate.edu. The models computed with CAPTURE can now be done with Program MARK, and CAPTURE is actually distributed as part of MARK. For further information, contact Ken Burnham or Gary White.
DISTANCE
DISTANCE provides an analysis of distance sampling data to estimate density and abundance of a population. Considerably more detail is provided in the above link, with the software and an electronic manual. The methods used by this program are documented in:
Buckland, S. T., D. R. Anderson, K. P. Burnham, and J. L. Laake. 1993. Distance sampling: estimating abundance of biological populations. Chapman & Hall, London. 446 pp.
Laake, J. L., S. T. Buckland, D. R. Anderson, and K. P. Burnham. 1994. DISTANCE User’s Guide V2.1. Colorado Cooperative Fish & Wildlife Research Unit, Colorado State University, Fort Collins, CO. 84 pp.
Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L.
Borchers, and L. J. Thomas. 2001. An Introduction to Distance Sampling: Estimating Abundance of Biological Populations. Oxford University Press, Oxford, UK. 432 pp.
Thomas, L., S. T. Buckland, K. P. Burnham, D. R. Anderson, J. L.
Laake, D. L. Borchers, and S. Strindberg. 2002. Distance sampling. Pp.
544-552, Volume 1, in Encyclopedia of Environmetrics, El-Shaarawi, A.
H. and W. W. Piegorsh (Eds). John Wiley and Sons Ltd. Chichester.
Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L.
Borchers, L. J. Thomas (Editors). 2004. Advanced Distance Sampling. Oxford University Press, Oxford, UK.
A web site with info about program DISTANCE:
Thomas, L., Laake, J.L., Strindberg, S., Marques, F.F.C., Buckland,
S.T., Borchers, D.L., Anderson, D.R., Burnham, K.P., Hedley, S.L., and
Pollard, J.H. 2002. Distance 4.0. Release 1. Research Unit for Wildlife Population Assessment, University of St. Andrews, UK.
http://www.ruwpa.st-and.ac.uk/distance/
For further information, contact Ken Burnham or Jeff Laake.
ESTIMATE
ESTIMATE computes survival estimates from banding (ringing) recovery data from adult animals only. The methods and user’s manual are documented in:
The source code, executable for DOS, and example input files are included in the zip file. The models computed with this code can now be done with Program MARK, and continued use of ESTIMATE is not recommended. For further information, contact Gary White.
NOREMARK
NOREMARK is an old DOS program, and does not run under Windows 7. Instead of using the NOREMARK software, you should use Program MARK and the mark-resight estimators therein. Details of these estimators are provided in Chapter 18 of the MARK Gentle Introduction.
NOREMARK computes estimates of population size for a population with a known number of marked animals and 1 or more resighting occasions. The major citation for the program is:
White, G. C. 1996. NOREMARK: population estimation from mark-resighting surveys. Wildlife Society Bulletin. 24:50-52.
Four different estimators are provided: joint hypergeometric maximum likelihood, immigration/emigration joint maximum likelihood, Minta-Mangel bootstrap procedure, and Bowden’s estimator. Simulation procedures for determining estimator performance and necessary sample sizes are also provided. The user’s manual for the program is provided as a WordPerfect document in the zip file, along with numerous input examples. For further information, contact Gary White. A problem with the profile likelihood estimates for the joint hypergeometric estimator was fixed on 30 January 1996. Corrections to the confidence intervals for Bowden’s estimator were made on 12 September, 2002. The number of marked animals minus one is now used for the degrees of freedom of the t statistic, and the lower CI was rounded up to the next integer and the upper CI was rounded down to the next integer.
RELEASE
RELEASE computes survival estimates and goodness-of-fit tests for a large class of survival experiments based on capture-recapture of marked populations. The general model is the Cormack-Jolly-Seber model for each experimental group (survival and capture probabilities different for each group), with a progression of submodels to the null model of the same survival and capture probabilities for all groups. Details of the procedures and a user’s manual are provided in:
Contained in the RELEASE.ZIP file are RELEASE.EXE to run interactively in DOS, plus example input files from the AFS Monograph. Another file available via anonymous ftp for handling larger jobs is REL_32.EXE to batch process in Windows 95 and NT. Note that the Windows 95 and NT version does not have the interactive interface provided in the RELEASE.ZIP file. FORTRAN source code for RELEASE is provided in relsrc.zip. All the models computed with RELEASE can now be done with Program MARK, and continued use of RELEASE is not recommended, except possibly for investigating the goodness-of-fit of a model and some simulations. RELEASE is distributed as part of Program MARK for this reason. For further information, contact Gary White.
Radio-tracking Programs
All the software except SURVIV (listed below) described in
White, G. C., and R. A. Garrott. 1990. Analysis of wildlife radio-tracking data. Academic Press, San Diego, CA. 383 pp.
is included in this zip file. Source code for the FORTRAN programs, executable files, SAS code, and input examples are provided. Be sure to use the -d option of pkunzip so that the subdirectory RADIOTRK and all its subdirectories are created when you unzip the radiotrk.zip file. Documentation for this software is provided in the book listed above. For further information, contact Gary White.
SURVIV
SURVIV is a FORTRAN code to compute survival estimates from general multinomial models. To run this program, you must have a FORTRAN compiler, because the model must be compiled into the SURVIV executable. A reference on the program is:
White, G. C. 1983. Numerical estimation of survival rates from band-recovery and biotelemetry data. Journal of Wildlife Management 47:716-728.
A user’s manual for the program and example input are provided in:
White, G. C., and R. A. Garrott. 1990. Analysis of wildlife radio-tracking data. Academic Press, San Diego, CA. 383 pp.
The Microsoft FORTRAN version of SURVIV is available as ms-surv .zip . The Ryan-McFarland FORTRAN version of SURVIV is available as rm-surv.zip . Both zip files contain DOS batch files to demonstrate how the program should be set up, example input, and a user’s manual in WordPerfect format. For further information, contact Gary White.
Stochastic Dynamic Programming (SDP)
Software and user’s guide for the stochastic dynamic programming package:
Lubow, B. C. 1995. SDP: Generalized software for solving stochastic dynamic optimization problems. Wildlife Society Bulletin 23:738-742.
For more information, contact Bruce Lubow.
For other sources of software related to wildlife, see the WWW page of the llinois Natural History Survey, the Population Analysis Software Group, The Wildlife Society’s Computer Software Exchange, or Evan Cooch’s software page. In addition, you can execute the Schwarz-Arnason model (i.e., POPAN) online at http://www.stat.sfu.ca/~cschwarz/Carlan.online/.
For questions or comments: Gary White
To see the home pages of the folks involved in developing this software:
Last Modified 05/16/17
Gary White /gwhite@cnr.colostate.edu
This page has been accessed times since August 16, 2000.
Last modified