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)

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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. 

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Installation
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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

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Troubleshooting
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# 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. 

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Files
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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)

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History
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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

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Known bugs, problems and limitations
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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

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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
