DENSITY Version 4.1.2
14 December 2007

Copyright (c) 2007 Murray Efford

Spatially explicit capture-recapture estimation of animal population density
www.otago.ac.nz/density
Email density.software@otago.ac.nz

============================================================================

This is the first release of Version 4 and you may find minor bugs or errors 
in the documentation. Please let me know. 

============================================================================

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 2007, Efford et al. in press). 

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.

============================================================================

Files

DENSITY4.EXE		The program executable
DENSITY4.chm    	Compiled HTML Help file for version 4
README4.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 4.1.1
28 11 2007 Build 4.1.1.13  First release of Density 4.1
30 11 2007 Build 4.1.1.16  Minor interface bugs fixed, and improved Help
01 12 2007 Build 4.1.1.18  Improved point and click selection in trap map
                           Input sequence of detections within occasions is 
                           now retained for plotting tracks and 'list captures'
                           Maximum occasions up from 50 to 100 (trial only)
                           Scrollbars now working on 'list captures'
Release 4.1.2
03 12 2007 Build 4.1.2.1   Trap Builder 'Input from file' allows random
                           subsample of trap sites, including GRTS
			   Optionally discard captures from trap sites that do 
                           not appear in current trap layout (default is error msg)
                           Fixed bug in display of open population estimates
	                   ML SECR standalone likelihood evaluation mesh x2 
04 12 2007 Build 4.1.2.3   Trap Builder limit on number of sites raised to 1000000
11 12 2007 Build 4.1.2.13  Fixed bug in ML SECR (allow varying number of traps 
                           between sessions)
                           Minor changes to Help
                           New features (experimental):
                           - jackknife variance between grids (sessions)
                           - resample capture file for PowerAnalysis
14 12 2007 Build 4.1.2.14  Improvements
                           - area units now apply to esa 
                           - PowerAnalysis dynamic population resampling now 
                             combines with dynamic trap subsampling
                           New features
                           - PowerAnalysis subsampling with replacement
                           - data menu : export filtered captures
                           

============================================================================

Installation
============================================================================

Density 4 runs on Windows 95 and above. 
It has not been tested on Windows Vista.
Screen size should be at least 1024 x 768, but preferably 1280 x 1024

No special installation is required.
Copy all files to one folder
Create a shortcut to density4.exe

============================================================================

References
Borchers DL, Efford MG 2007. Spatially explicit maximum likelihood methods 
  for capture-recapture studies. 
  Biometrics (OnlineEarly doi:10.1111/j.1541-0420.2007.00927.x)
Efford MG 2004. Density estimation in live-trapping studies. 
  Oikos 106: 598-610.
Efford MG, Borchers DL, Byrom AE In press. Density estimation by spatially 
  explicit capture-recapture: likelihood-based methods. Environmental and 
  Ecological Statistics.
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

Zoology Department
University of Otago, 
PO Box 56,
Dunedin,
NEW ZEALAND

murray.efford@otago.ac.nz
