DENSITY Version 5.0.3 21 April 2014 Copyright (c) 2007-2014 Murray Efford Spatially explicit capture-recapture estimation of animal population density Website www.otago.ac.nz/density Support forum www.phidot.org/forum/index.php (look there for latest FAQ) ============================================================================ DENSITY is a Windows application for the analysis of capture-recapture data located in space. It implements new methods for estimating absolute population density from closed population samples (Efford 2004, Efford et al. 2004, Borchers & Efford 2008, Efford, Borchers & Byrom 2009, Efford, Dawson & Borchers 2009). DENSITY also provides a graphical interface for calculating other capture- recapture estimates as well as tools for graphing capture locations and calculating the conventional effective trapping area of a grid by the boundary strip method. * Please let me know if you find bugs or errors in the program or documentation. ============================================================================ Installation ============================================================================ Density 5 runs on Windows XP and above. Version 5.0 has not been tested on Windows 8. Please report any problems. Screen size should be at least 1024 x 768, but preferably 1280 x 1024 Density 5 is supplied as a single zip file. No special installation is required. Unzip (extract) all files to one folder Create a shortcut to density5.exe ============================================================================ Troubleshooting ============================================================================ # I cannot open the help file. What is wrong? Density5.chm is a compiled Windows help file, created with the Microsoft help compiler. It is seen by the operating system as an executable file, and treated by some systems as a security risk. This is the most likely cause of your problem. Try opening the help file from Windows Explorer and overriding any security warning. ============================================================================ Files ============================================================================ DENSITY5.EXE The program executable DENSITY5.chm Compiled HTML Help file for version 4 README5.TXT This file trap.txt Demonstration trap file capt.txt Demonstration capture file ovtrap.txt Example Orongorongo possum trap layout ov4954.txt Example Orongorongo possum captures 1996-1997 ovmask.txt Example Orongorongo habitat mask ovimage.jpg Example Orongorongo background image (left 2674490, right 2675460, bottom 5982250, top 5983090) Bend H1 LCR capt.txt Example ferret capture data Bend H1 LCR gps.txt Example ferret trap layout data webcapt.txt Example Data of Parmenter et al 2003 website.txt Example Trap file for use with data of Parmenter et al 2003 removalgrid.txt Example Removal grid of Parmenter et al 2003 breeding6172Top10.txt Chan Robbins' mist netting data (Efford et al. 2004) netsites6172.txt Trap file for use with mist netting data matakicaptures.txt Stoat DNA microsatellite data of Andrea Byrom (see Efford, Borchers & Byrom in press) matakitraps.txt Trap file for use with stoat DNA data JLYEXMPLC.txt Nichols et al Microtus data (nonspatial) snowshoe.txt Burnham & Cushwa snowshoe hare dataset s-drawb.exe Program for GRTS sampling (McDonald 2004) (Other demonstration files may be included) ============================================================================ History ============================================================================ Release 4.1 28 11 2007 Release 4.2 23 09 2008 Release 4.3 15 11 2008 Release 4.4 19 04 2009 Release 5.0 beta 05 12 2012 Release 5.0.2 15 01 2013 Release 5.0.3 21 04 2014 fixed bug when mesh trimmed with 'trap buffer' option ============================================================================ Known bugs, problems and limitations ============================================================================ ML SECR bootstrap remains experimental Over-ambitious analyses of small datasets can cause the program to hang or leak memory, especially with finite-mixture models in ML SECR. ML SECR within-session time covariates are assumed to apply across all sessions ============================================================================ References (see www.otago.ac.nz/density/publications.html for some of these) ============================================================================ Borchers DL, Efford MG 2007. Supplements to Biometrics paper. Available online at www.otago.ac.nz/density/publications.html Borchers DL, Efford MG 2008. Spatially explicit maximum likelihood methods for capture-recapture studies. Biometrics 64: 377-385. Efford MG 2004. Density estimation in live-trapping studies. Oikos 106: 598-610. Efford MG, Borchers DL, Byrom AE 2009. Density estimation by spatially explicit capture-recapture: likelihood-based methods. Pp. 255-269 In: DL Thompson, EG Cooch, MJ Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer, New York. Efford MG, Dawson DK, Borchers, DL 2009. Population density estimated from locations of individuals on a passive detector array. Ecology 90: 2676-2682 Efford MG, Dawson DK, Robbins CS 2004. DENSITY: software for analysing capture-recapture data from passive detector arrays. Animal Biodiversity and Conservation 27: 217-228. McDonald T 2004. GRTS for the Average Joe: A GRTS Sampler for Windows. www.west-inc.com/computer.php Accessed 22/12/06. Parmenter RR, Yates TL, Anderson DR, Burnham KP, Dunnum JL, Franklin AB, Friggens MT, Lubow BC, Miller M, Olson GS, Parmenter CA, Pollard J, Rexstad E, Shenk TM, Stanley TR, White GC 2003. Small-mammal density estimation: A field comparison of grid-based vs. web-based density estimators. Ecological Monographs 73: 1-26. Murray Efford Department of Mathematics and Statistics University of Otago, PO Box 56, Dunedin, NEW ZEALAND murray.efford@otago.ac.nz