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## EESC *Software Archive*

The following programs were developed at EESC and elsewhere for the analysis of animal populations for wildlife biologists/managers.  
ProgramDescriptionsoftware/band2js.html>BAND2Computes 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.software/brownie.html>BROWNIEComputes estimates of survival and recovery rates for 2-age class band-recovery data.software/capquota.html>CAPQUOTAComputes expected coefficients of variation of survival and capture probability for use in the design of capture-recapture-resighting experiments.software/capture.html>CAPTUREComputes estimates of capture probability and population size for "closed" population capture-recapture data.software/centroid.html>CENTROIDTests the null hypothesis that two samples of recoveries belong to the same bivariate distribution.software/comdyn.html>COMDYNComputes estimates of species richness using large scale data.software/contrast.html>CONTRASTCompares estimates of survival (or any normally distributed parameter estimates).software/CountRemoval.html>CountRemovalA removal model for estimating detection probabilities from point count surveys.software/dosecomp.html>DOSECOMPAnalyzes dose responses for two populations, using the PROBIT model and the abbreviated protocol as described by Link et al(1996).software/dobserv.html>DOBSERVA Double-observer approach for estimating detection probability and abundance from avian point counts as described in Nichols et. al. (2000).software/estimate.html>ESTIMATEComputes estimates of survival and recovery rates for 1-age class band-recovery data.software/fatalityCMR.html>fatalityCMREstimates fatalities using raw counts of wildlife fatalities, trial experiments for carcass detection probability and persistence time.software/gencaph1.html>GENCAPH1Generates capture-history data for given s,theta,p,c.software/jolly.html>JOLLYComputes estimates of survival and capture probability for 1-age class open population capture-recapture models.software/jollyage.html>JOLLYAGEComputes estimates of survival and capture probability for 2-age class open population capture-recapture models.software/lolasurviv.html>LOLASURVIVComputes estimates of survival and capture probability for open capture-recapture models when sex is not allways known.software/mayfield.html>MAYFIELDComputes estimates of daily survival rate for nest visitation data.software/mssurviv.html>MSSURVIVComputes estimates of survival-movement and capture probability for open capture-recapture models.software/mssrvrd.html>MSSRVRD(BETA) replacement for MSSURVIV, RDSURV - Combines multi-strata, robust-design and trap-deaths.software/mssrvrcv.html>MSSRVRCVComputes survival-movement, capture and recovery probabilities from multi-strata capture-recapture-recovery data.software/mssrvmis.html>MSSRVMISComputes estimates of survival and capture probability adjusted for missclassification.software/mult.html>MULTComputes estimates of survival and recovery rates for band-recovery data with additional models for estimating reporting rate.software/nestAbund.html>nestAbundEstimates abundance of nests using a capture-recapture approach which deals with imperfect detection probability as well as the impact of environmental and individual covariates on nest fate.software/ordsurviv.html>ORDSURVIVComputes estimates of survival and temporary emigration under the "Open Robust Design".software/power.html>POWERComputes the power of between-model likelihood ratio tests.software/presence.html>PRESENCEEstimates patch occupancy rates and related parameters.software/rdsurviv.html>RDSURVIVComputes estimates of survival and capture probability using capture-recapture data with "robust-design" models and recoveries.software/release.html>RELEASEComputes estimates of survival and capture probability for capture-recapture experiments on open animal populations.software/scatman.html>SCATMANTests the hypothesis of prey-selectivity based on random samples of predator scats.software/spacecap.html>SPACECAPEstimates Animal Abundance and Density using Spatially-Explicit Capture-Recapture.software/specrich.html>SPECRICHComputes "species richness" or total number of species from emperical species abundance distribution data.software/specrich2.html>SPECRICH2Estimates the total number of species from species presence-absence data on multiple sample sites or occasions using model M(h) from program *CAPTURE*.software/surviv.html>SURVIVComputes estimates of survival (or any model parameter) with  multinomially distributed data.software/tmsurviv.html>TMSURVIVComputes estimates of survival and capture probability and the proportion of *transients* in open population capture-recapture data.Other www sites with wildlife-related software:- Colorado State University Department of Fishery and Wildlife Biology MARK
Population Analysis Software Group
 POPAN
www.PhiDot.Org
 (Evan Cooch's) software page.
/www.mrc-bsu.cam.ac.uk/software/bugs/>www.mrc-bsu.cam.ac.uk/software/bugs/
  WINBUGS - Basian inference Using Gibbs Sampling.
Disclaimer:Although this program has been used by the U.S. Geological Survey (USGS), no	warranty, expressed or implied, is made by the USGS or the U.S. Government as	to the accuracy and functioning of the program and related program material nor	shall the fact of distribution constitute any such warranty, and no responsibility is	assumed by the USGS in connection therewith.
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 are sample citations for two of the programs:  - Hines, J. E. (2006). PRESENCE- Software to estimate patch occupancy        and related parameters. USGS-EESC.        http://www.mbr-pwrc.usgs.gov/software/presence.html.  
            Hines, J. E. (1996). *SPECRICH Software to compute species abundance            from emperical species abundance distribution data. USGS-EESC.             http://www.mbr-pwrc.usgs.gov/software/specrich.html.  Program SURVIV requires a FORTRAN compiler to generate the user-definedestimation routine.  If you do not have one, click /directory.fsf.org/wiki/Gfortran>here to download the *FREE Gnu FORTRAN compiler for WINDOWS.
A good, free ascii text editor (Notepad++) can be downloaded /notepad-plus-plus.org>here.
This list is maintained by:
Jim Hines (jhines@usgs.gov)Eastern Ecological Science Center12100 Beech Forest RdLaurel, Md 20708-4030
Last updated: 31-May-2017**