DENSITY Version 3.3
11 Apr 2005
13 Oct 2005 (3.3.1.7)

Spatially explicit capture-recapture estimation
of animal population density

Copyright (C) 2004, 2005 Landcare Research Ltd

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

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation, Version 2.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.

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

DENSITY is a Microsoft Windows application for the analysis of
capture-recapture data located in space. It implements a new method for
estimating absolute population density from closed population samples (Efford 
2004, Efford et al. 2004, Efford et al. 2005). 

DENSITY also provides a simple graphical interface for calculating 
other capture-recapture estimates (Otis et al. 1978; Pollock et al. 1990 etc.) 
as well as tools for graphing capture locations and calculating the 
conventional effective trapping area of a grid by the boundary strip method.

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

Files

DENSITY3.EXE		The program executable
DENSITY3.chm    	Compiled HTML Help file for version 3.3
README33.TXT		This file
NewfeaturesV32.htm	List of new features in version 3.2
ChangesV33.htm       	List of changes in version 3.3

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
OVHAB10.EPP		Example habitat mask
GREEN.CLR		Colour file for mask

Bend H1 LCR capt.txt	Ferret example capture data
Bend H1 LCR gps.txt	Ferret example trap layout data

JLYEXMPLC.txt		Nichols et al Microtus data (nonspatial)
snowshoe.txt		Burnham & Cushwa snowshoe hare dataset

Breeding6172Top10.txt	Chan Robbins' mist netting data (see Efford et al. 2004)
netsites6172.txt        Trap file for use with mist netting data

webcapt.txt           	Data of Parmenter et al 2003
website.txt           	Trap file for use with data of Parmenter et al 2003
removalgrid.txt      	Removal grid of Parmenter et al 2003

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

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

Density 3.3 runs on Windows 95 and above.
Screen size should be at least 1024 x 768.

No special installation is required.
Copy all files to one folder
Create a shortcut to density3.exe


Critical changes in Version 3.2 over Version 2.1
=========================================================================================

The basic format remains similar to 2.1, but there have been many many minor changes and files saved 
from 2.1 (.den, .dpa) cannot be expected to work.

An interface is provided to Distance (Thomas et al.) for analysing trapping webs and 'passive transects'. 
This works only if one of the Distance executables (mcds.exe, d4.exe, d35engine.exe) can be found - DENSITY
looks in the obvious 'Program files' folders and in the directory from which DENSITY is called.

An interface is also provided to Capture (Otis et al. 1978; see also http://www.mbr-pwrc.usgs.gov/software.html)

Default settings have changed. 
The default population dispersion for inverse prediction is now 'Poisson' rather than 'Even'
The default movement statistic is now the square root of the pooled spatial variance (RPSV)

Many new features have been added. Most are listed in 'new features.chm' (or see Help)

=======================================================================================================
Changes in Version 3.3 over Version 3.2

23 12 04 Revised help file for confidence intervals
23 12 04 Added PA field TrueB for actual number of new animals in population at next session
28 12 04 Minor changes to calculation of stopover duration fields
29 12 04 Added PA fields JSBeta and seJSBeta for Schwarz & Arnason beta 
30 12 04 Increased width for some open-population fields on output

18 02 05 Enhanced control of integration buffer in MLE of density
28 02 05 Fixed bug in 'target values' interface
01 03 05 The initial values panel has been hidden on the main screen. Initial values are now set exclusively on the Inverse Prediction page in Options. The default setting has been changed to 'Auto'. Coding has been streamlined, so some bugs may yet appear.
01 03 05 Power analysis fields AutoD, Autog0, AutoSig now record the actual values used for IP or ML at each replicate, rather than values from a separate call to the algorithm.

18 03 05 Fixed bug in Poweranalysis : output an open population header even when turnover was disabled
18 03 05 New feature: Tools | Preview option in Power analysis shows simulation settings that will be used
18 03 05 Fixed bug in Poweranalysis : Now uses correct title line for simulation output (i.e. from PowerAnalysis page in Options)
22 03 05 Output header for Distance analyses now records Monotonicity
22 03 05 Double click session selector to return to first session
22 03 05 Display read-only initial values in memo field on main form; double-click to change
25 03 05 Increased number of decimal places in output of MLg0, and increased field width IPTime
30 03 05 Negative exponential detection function offered as an option
30 03 05 Fixed bug that caused Invalid FP operation when 'Auto initial values' selected with 'Uniform' detection model
31 03 05 Zippin closed-population estimator re-enabled with correct failure criterion (Seber 1982 p.502)
31 03 05 Added trapping web (Parmenter et al 2003) and mist netting (C. S. Robbins) example datasets
01 04 05 Increased default absolute tolerance for minimisation of log likelihood from 0.00001 to 0.001
02 04 05 New field 'DetectFn' to record detection function used in analysis
02 04 05 Adjustments to layout of MLE Options page
02 04 05 Added check for traps in masked non-habitat
06 04 05 Power Analysis added field CumTS% for cumulative percentage of traps visited over trapping session
06 04 05 Power Analysis added 'Export captures' format for cumulative count of sites visited over occasions within a Session
06 04 05 Power Analysis Log and Output tool buttons now enabled from the beginning
06 04 05 Power Analysis 'Trap success' field TS% now enabled from the beginning
09 04 05 SpotSim bug fixed (Dosim2 needed valid dummy for target)
10 04 05 Ctrl-T (Transfer to PowerAnalysis) bugs fixed
10 04 05 Minor TrapBuilder bug (colour of traps as dots) fixed
10 04 05 Bug in loadfile fixed
10 04 05 Bug in selection of output fields fixed
10 04 05 Closure statistic moved within output fields to precede all spatial statistics
11 04 05 Choice of MARK or plain format for export of capture histories
11 04 05 'Fields in output' button added to main form
12 04 04 VERSION 3.3.1.1

26 06 05 Log likelihood of closed population estimators has added constant
14 07 05 Increased output precision of IPDens to 5 dp
31 08 05 Bug in PowerAnalysis fixed: previously did not take phi for open populations from stack
01 09 05 Field selector in PowerAnalysis corrupted - bug fixed but further testing needed
01 09 05 BUILD 3.3.1.4
01 09 05 Bug in PowerAnalysis fixed - previously gave pointer error when cursor crossed bottom of statselector box
06 09 05 Further patch to field selection in PowerAnalysis - now ML fields remain active when selected
06 09 05 BUILD 3.3.1.5
12 09 05 Corrected bug in matrix multiplication for variance of conditional likelihood estimates of density
13 09 05 PowerAnalysis now reports deviance MLDev for conditional likelihood model 
         (but still does not simulate GOF test - too time consuming)
14 09 05 BUILD 3.3.1.6
14 09 05 PowerAnalysis: Fixed bug in coverage of g0, sigma
13 10 05 TrapBuilder now displays error message when user attempt to place more than the maximum number of traps (1200)
13 10 05 BUILD 3.3.1.7
=======================================================================================================

References
Efford MG 2004. Density estimation in live-trapping studies. Oikos 106: 598-610.
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. 
Efford MG, Warburton B, Coleman MC, Barker RJ 2005. A field test of two methods for density 
  estimation. Wildlife Society Bulletin 33: 731-738.
Otis DL, Burnham KP, White GC, Anderson DR 1978. Statistical inference from capture data on 
  closed animal populations. Wildlife Monographs No. 62.
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.
Pollock KH, Nichols JD, Brownie C, Hines JE 1990. Statistical inference for capture-recapture 
  experiments. Wildlife Monographs No. 107.

Murray Efford

Landcare Research, 
Private Bag 1930, 
Dunedin,
NEW ZEALAND

effordm@landcareresearch.co.nz

12 Apr 2005
26 Jun 2005
14 Jul 2005
01 Sep 2005
14 Sep 2005
13 Oct 2005
