{"id":170,"date":"2017-04-18T01:47:45","date_gmt":"2017-04-18T01:47:45","guid":{"rendered":"http:\/\/sites.warnercnr.colostate.edu\/gwhite\/?page_id=170"},"modified":"2017-05-19T18:32:52","modified_gmt":"2017-05-19T18:32:52","slug":"software","status":"publish","type":"page","link":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/software\/","title":{"rendered":"Software"},"content":{"rendered":"

Software Developed by<\/span><\/span><\/h2>\n

Department of Fishery and Wildlife Biology<\/a> and<\/span><\/span><\/h2>\n

Colorado Coop. Fish and Wildlife Unit<\/a>,<\/span><\/span><\/h2>\n

Colorado State University <\/a><\/span>
\n<\/span><\/h2>\n

\u00a0\u00a0\u00a0 Most of the files provided on this page require pkunzip<\/a> to unzip them.<\/span><\/p>\n

\u00a0\u00a0\u00a0 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.\u00a0 The following sites provide information on how to cite electronic documents: MLA-Style Citations of Electronic Sources<\/a> and Electronic Sources: APA Style of Citation<\/a> .<\/span><\/p>\n

<\/p>\n

<\/a>Program MARK<\/b><\/a><\/span><\/h3>\n

Program MARK is a new software package currently being developed. \u00a0 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.\u00a0 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.\u00a0 Check out the description of its capabilities, or information on how to download the program.<\/span><\/big><\/p>\n

<\/p>\n

<\/a>BROWNIE<\/a><\/b><\/span><\/h3>\n

BROWNIE computes survival estimates from banding (ringing) recovery data from young and adult animals. The methods and user’s manual are documented in:<\/p>\n

Brownie, C., D. R. Anderson, K. P. Burnham, and D. S. Robson. 1985. Statistical inference from band recovery data — a handbook. U. S. Department of Interior, Fish and Wildlife Service Resource Publication 156. 305 pp. <\/a><\/p>\n

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<\/a>, and continued use of BROWNIE is not recommended. For further information, contact Gary White<\/a>.<\/p>\n

<\/p>\n

<\/a>CAPTURE<\/a><\/span><\/h3>\n

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:<\/p>\n

Otis, D. L., K. P. Burnham, G. C. White, and D. R. Anderson. 1978. Statistical inference from capture data on closed animal populations. Wildlife Monographs 62. 135 pp.<\/a><\/p>\n

White, G. C., D. R. Anderson, K. P. Burnham, and D. L. Otis. 1982. Capture-recapture and removal methods for sampling closed populations.Los Alamos National Laboratory LA-8787-NERP. 235 pp. <\/a><\/p>\n

The latter document contains a user’s manual (Appendix A<\/a>) and numerous examples for CAPTURE.\u00a0 An interactive interface (2CAPTURE) is available from Dr. Kenneth Burnham at the same address (and includes its own 2CAPTURE manual<\/a>), or via email to kenb@lamar.colostate.edu<\/a>. \u00a0 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<\/a>. The models computed with CAPTURE can now be done with Program MARK<\/a>, and CAPTURE is actually distributed as part of MARK.\u00a0 For further information, contact Ken Burnham<\/a> or Gary White<\/a>.<\/p>\n

<\/p>\n

<\/a>DISTANCE<\/span><\/a><\/h3>\n

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:<\/p>\n

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.<\/p>\n

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.<\/p>\n

Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L.
\nBorchers, and L. J. Thomas. 2001. An Introduction to Distance Sampling: Estimating Abundance of Biological Populations.\u00a0 Oxford University Press, Oxford, UK. 432 pp.<\/p>\n

Thomas, L., S. T. Buckland, K. P. Burnham, D. R. Anderson, J. L.
\nLaake, D. L. Borchers, and S. Strindberg. 2002. Distance sampling. Pp.
\n544-552, Volume 1, in Encyclopedia of Environmetrics, El-Shaarawi, A.
\nH. and W. W. Piegorsh (Eds). John Wiley and Sons Ltd. Chichester.<\/p>\n

Buckland, S. T., D. R. Anderson, K. P. Burnham, J. L. Laake, D. L.
\nBorchers, L. J. Thomas (Editors). 2004. Advanced Distance Sampling. Oxford University Press, Oxford, UK.<\/p>\n

A web site with info about program DISTANCE:
\nThomas, L., Laake, J.L., Strindberg, S., Marques, F.F.C., Buckland,
\nS.T., Borchers, D.L., Anderson, D.R., Burnham, K.P., Hedley, S.L., and
\nPollard, J.H. 2002. Distance 4.0. Release 1. Research Unit for Wildlife Population Assessment, University of St. Andrews, UK.<\/p>\n

http:\/\/www.ruwpa.st-and.ac.uk\/distance\/<\/a><\/p>\n

For further information, contact Ken Burnham<\/a> or Jeff Laake<\/a>.<\/p>\n

<\/p>\n

<\/a>ESTIMATE<\/a><\/span><\/h3>\n

ESTIMATE computes survival estimates from banding (ringing) recovery data from adult animals only. The methods and user’s manual are documented in:<\/p>\n

Brownie, C., D. R. Anderson, K. P. Burnham, and D. S. Robson. 1985. Statistical inference from band recovery data — a handbook. U. S. Department of Interior, Fish and Wildlife Service Resource Publication 156. 305 pp<\/a>.<\/p>\n

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<\/a>, and continued use of ESTIMATE is not recommended. For further information, contact Gary White<\/a>.<\/p>\n

<\/p>\n

<\/a>NOREMARK<\/a><\/span><\/h3>\n

NOREMARK is an old DOS program, and does not run under Windows 7. Instead of using the NOREMARK software, you should use Program MARK<\/a> and the mark-resight estimators therein. Details of these estimators are provided in Chapter 18 of the MARK Gentle Introduction.<\/a><\/p>\n

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:<\/p>\n

White, G. C. 1996. NOREMARK: population estimation from mark-resighting surveys. Wildlife Society Bulletin. 24:50-52.<\/p>\n

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<\/a> 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>.\u00a0 A problem with the profile likelihood estimates for the joint hypergeometric estimator was fixed on 30 January 1996.\u00a0 Corrections to the confidence intervals for Bowden’s estimator were made on 12 September, 2002.\u00a0\u00a0 The number of marked animals minus one is now used for the degrees of freedom of the t<\/i> statistic, and the lower CI was rounded up to the next integer and the upper CI was rounded down to the next integer.<\/p>\n

<\/p>\n

<\/a>RELEASE<\/a><\/span><\/h3>\n

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:<\/p>\n

Burnham, K. P., D. R. Anderson, G. C. White, C. Brownie, and K. H. Pollock. 1987. Design and analysis methods for fish survival experiments based on release-recapture. American Fisheries Society Monograph 5. 437 pp. <\/a><\/p>\n

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<\/a> 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<\/a> file. FORTRAN source code for RELEASE is provided in relsrc.zip<\/a>.\u00a0 All the models computed with RELEASE can now be done with Program MARK<\/a>, and continued use of RELEASE is not recommended, except possibly for investigating the goodness-of-fit of a model and some simulations.\u00a0 RELEASE is distributed as part of Program MARK<\/a> for this reason.\u00a0 For further information, contact Gary White<\/a>.<\/p>\n

<\/p>\n

<\/a>Radio-tracking Programs<\/a><\/span><\/h3>\n

All the software except SURVIV (listed below) described in<\/p>\n

White, G. C., and R. A. Garrott. 1990. Analysis of wildlife radio-tracking data. Academic Press, San Diego, CA. 383 pp.<\/p>\n

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<\/a> file. Documentation for this software is provided in the book listed above. For further information, contact Gary White<\/a>.<\/p>\n

<\/p>\n

<\/a>SURVIV<\/span><\/h3>\n

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:<\/p>\n

White, G. C. 1983. Numerical estimation of survival rates from band-recovery and biotelemetry data. Journal of Wildlife Management 47:716-728.<\/p>\n

A user’s manual for the program and example input are provided in:<\/p>\n

White, G. C., and R. A. Garrott. 1990. Analysis of wildlife radio-tracking data. Academic Press, San Diego, CA. 383 pp.<\/p>\n

The Microsoft FORTRAN version of SURVIV is available as ms-surv .zip <\/a>. The Ryan-McFarland FORTRAN version of SURVIV is available as rm-surv.zip <\/a>. 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<\/a>.<\/p>\n

<\/p>\n

<\/a>Stochastic Dynamic Programming (SDP<\/a>)<\/span><\/b><\/h3>\n

Software and user’s guide for the stochastic dynamic programming package:
\nLubow, B. C. 1995. SDP: Generalized software for solving stochastic dynamic optimization problems. Wildlife Society Bulletin 23:738-742.
\nFor more information, contact Bruce Lubow<\/a>.<\/p>\n

<\/p>\n

For other sources of software related to wildlife, see the WWW page of the llinois Natural History Survey<\/a>, the <\/a>Population Analysis Software Group<\/a>, The Wildlife Society’s <\/a>Computer Software Exchange<\/a>, or <\/a>Evan Cooch’s<\/a> software page.\u00a0 In addition, you can execute the Schwarz-Arnason model (i.e., POPAN) online at http:\/\/www.stat.sfu.ca\/~cschwarz\/Carlan.online\/<\/a>.<\/p>\n

<\/p>\n

For questions or comments: Gary White<\/a><\/p>\n

<\/p>\n

To see the home pages of the folks involved in developing this software:<\/p>\n

Gary C. White<\/a><\/p>\n

Kenneth P. Burnham<\/a><\/p>\n

David R. Anderson<\/a><\/p>\n

Last Modified 05\/16\/17
\nGary White \/gwhite@cnr.colostate.edu<\/p>\n

<\/p>\n

This page has been accessed times since August 16, 2000.<\/p>\n

Last modified<\/p>\n","protected":false},"excerpt":{"rendered":"

Software Developed by Department of Fishery and Wildlife Biology and Colorado Coop. Fish and Wildlife Unit, Colorado State University \u00a0\u00a0\u00a0 Most of the files provided on this page require pkunzip to unzip them. \u00a0\u00a0\u00a0 One of the problems with obtaining …<\/p>\n

Software<\/span> Read More »<\/a><\/p>\n","protected":false},"author":117,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-170","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/170","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/users\/117"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/comments?post=170"}],"version-history":[{"count":17,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/170\/revisions"}],"predecessor-version":[{"id":470,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/170\/revisions\/470"}],"wp:attachment":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/media?parent=170"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}