Patuxent Software Archive

PWRC Software Archive

The following programs were developed at PWRC and elsewhere for the analysis of animal populations for wildlife biologists/managers.

Program Description
BAND2 Computes the number of animals that must be banded in order to achieve a specified level of precision for survival rates estimated using band recovery models.

BROWNIE Computes estimates of survival and recovery rates for 2-age class band-recovery data.

CAPQUOTA Computes expected coefficients of variation of survival and capture probability for use in the design of capture-recapture-resighting experiments.

CAPTURE Computes estimates of capture probability and population size for "closed" population capture-recapture data.

CENTROID Tests the null hypothesis that two samples of recoveries belong to the same bivariate distribution.

COMDYN Computes estimates of species richness using large scale data.

CONTRAST Compares estimates of survival (or any normally distributed parameter estimates).

DISTANCE Allows design and analysis of distance sampling surveys to estimate density and abundance of a population.

DOSECOMP Analyzes dose responses for two populations, using the PROBIT model and the abbreviated protocol as described by Link et al(1996).

DOBSERV A Double-observer approach for estimating detection probability and abundance from avian point counts as described in Nichols et. al. (2000).

ECOSRCH ECOSEARCH was developed as a first step to a testable, scientific basis for ecosystem management.

ESTIMATE Computes estimates of survival and recovery rates for 1-age class band-recovery data.

GENCAPH1 Generates capture-history data for given s,theta,p,c.

GENPRES Generates patch-occupancy data and analyzes using MARK.

JOLLY Computes estimates of survival and capture probability for 1-age class open population capture-recapture models.

JOLLYAGE Computes estimates of survival and capture probability for 2-age class open population capture-recapture models.

LOLASURVIV Computes estimates of survival and capture probability for open capture-recapture models when sex is not allways known.

MARK Program MARK, a Windows 95, 98, or NT program, provides parameter estimates from marked animals when they are re-encountered at a later time. Click here to go to the MARK page.

MAYFIELD Computes estimates of daily survival rate for nest visitation data.

MSSURVIV Computes estimates of survival-movement and capture probability for open capture-recapture models.

MSSRVRD (BETA) replacement for MSSURVIV, RDSURV - Combines multi-strata, robust-design and trap-deaths.

MSSRVRCV Computes survival-movement, capture and recovery probabilities from multi-strata capture-recapture-recovery data.

MSSRVMIS Computes estimates of survival and capture probability adjusted for missclassification.

MULT Computes estimates of survival and recovery rates for band-recovery data with additional models for estimating reporting rate.

ORDSURVIV Computes estimates of survival and temporary emigration under the "Open Robust Design".

POWER Computes the power of between-model likelihood ratio tests.

PRESENCE Estimates patch occupancy rates and related parameters.

RDSURVIV Computes estimates of survival and capture probability using capture-recapture data with "robust-design" models and recoveries.

RELEASE Computes estimates of survival and capture probability for capture-recapture experiments on open animal populations.

SCATMAN Tests the hypothesis of prey-selectivity based on random samples of predator scats.

SPECRICH Computes "species richness" or total number of species from emperical species abundance distribution data.

SPECRICH2 Estimates the total number of species from species presence-absence data on multiple sample sites or occasions using model M(h) from program CAPTURE.

SURVIV Computes estimates of survival (or any model parameter) with multinomially distributed data.

TMSURVIV Computes estimates of survival and capture probability and the proportion of transients in open population capture-recapture data.

virttrap Instructional tool simulating a capture-recapture experiment.

WINBUGS Basian inference Using Gibbs Sampling.

Program	Description
BAND2	Computes the number of animals that must be banded in order to achieve a specified level of precision for survival rates estimated using band recovery models.
BROWNIE	Computes estimates of survival and recovery rates for 2-age class band-recovery data.
CAPQUOTA	Computes expected coefficients of variation of survival and capture probability for use in the design of capture-recapture-resighting experiments.
CAPTURE	Computes estimates of capture probability and population size for "closed" population capture-recapture data.
CENTROID	Tests the null hypothesis that two samples of recoveries belong to the same bivariate distribution.
COMDYN	Computes estimates of species richness using large scale data.
CONTRAST	Compares estimates of survival (or any normally distributed parameter estimates).
DISTANCE	Allows design and analysis of distance sampling surveys to estimate density and abundance of a population.
DOSECOMP	Analyzes dose responses for two populations, using the PROBIT model and the abbreviated protocol as described by Link et al(1996).
DOBSERV	A Double-observer approach for estimating detection probability and abundance from avian point counts as described in Nichols et. al. (2000).
ECOSRCH	ECOSEARCH was developed as a first step to a testable, scientific basis for ecosystem management.
ESTIMATE	Computes estimates of survival and recovery rates for 1-age class band-recovery data.
GENCAPH1	Generates capture-history data for given s,theta,p,c.
GENPRES	Generates patch-occupancy data and analyzes using MARK.
JOLLY	Computes estimates of survival and capture probability for 1-age class open population capture-recapture models.
JOLLYAGE	Computes estimates of survival and capture probability for 2-age class open population capture-recapture models.
LOLASURVIV	Computes estimates of survival and capture probability for open capture-recapture models when sex is not allways known.
MARK	Program MARK, a Windows 95, 98, or NT program, provides parameter estimates from marked animals when they are re-encountered at a later time. Click here to go to the MARK page.
MAYFIELD	Computes estimates of daily survival rate for nest visitation data.
MSSURVIV	Computes estimates of survival-movement and capture probability for open capture-recapture models.
MSSRVRD	(BETA) replacement for MSSURVIV, RDSURV - Combines multi-strata, robust-design and trap-deaths.
MSSRVRCV	Computes survival-movement, capture and recovery probabilities from multi-strata capture-recapture-recovery data.
MSSRVMIS	Computes estimates of survival and capture probability adjusted for missclassification.
MULT	Computes estimates of survival and recovery rates for band-recovery data with additional models for estimating reporting rate.
ORDSURVIV	Computes estimates of survival and temporary emigration under the "Open Robust Design".
POWER	Computes the power of between-model likelihood ratio tests.
PRESENCE	Estimates patch occupancy rates and related parameters.
RDSURVIV	Computes estimates of survival and capture probability using capture-recapture data with "robust-design" models and recoveries.
RELEASE	Computes estimates of survival and capture probability for capture-recapture experiments on open animal populations.
SCATMAN	Tests the hypothesis of prey-selectivity based on random samples of predator scats.
SPECRICH	Computes "species richness" or total number of species from emperical species abundance distribution data.
SPECRICH2	Estimates the total number of species from species presence-absence data on multiple sample sites or occasions using model M(h) from program CAPTURE.
SURVIV	Computes estimates of survival (or any model parameter) with multinomially distributed data.
TMSURVIV	Computes estimates of survival and capture probability and the proportion of transients in open population capture-recapture data.
virttrap	Instructional tool simulating a capture-recapture experiment.
WINBUGS	Basian inference Using Gibbs Sampling.

Other www sites with wildlife-related software:

Colorado State University Department of Fishery and Wildlife Biology.

icon llinois Natural History Survey

icon Population Analysis Software Group

icon Evan Cooch's software page.

Misc.

Citations - One of the problems with obtaining software from the Web is that hard copy documentation is not available. The following site provides information on how to cite electronic documents: MLA-Style Citations of Electronic Sources Here is a sample citation for one of the programs:
```
            Hines, J. E. (1996). SPECRICH Software to compute species abundance
            from emperical species abundance distribution data. USGS-PWRC. 
            http://www.mbr-pwrc.usgs.gov/software/specrich.html.
  
```
The programs are stored as "zip" archives. Most of the zip files contain both the source code (usually FORTRAN) and IBM-PC compatible executable files. If you need an unzipping program, you can download a free Windows unzipper [PowerArc] or a free MSDOS unzipper [unzip.exe].
Program SURVIV requires a FORTRAN compiler to generate the user-defined estimation routine. If you do not have one, click here to download the FREE Gnu FORTRAN compiler for WINDOWS 95/NT. Click here to download program SURVIV with the Gnu FORTRAN compiler.
A good, free ascii text editor (Notepad++) can be downloaded here for more information.

This list is maintained by:

Jim Hines 
Patuxent Wildlife Research Center
11510 American Holly Dr. #201
Laurel, Md 20708-4017                   Last updated: 09-July-2002