DENSITY Version 4.4.6
19 October 2010

Copyright (c) 2007-2010 Murray Efford

Spatially explicit capture-recapture estimation of animal population density

Website www.otago.ac.nz/density
Support forum www.phidot.org/forum (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 4 runs on Windows 95 and above. 
Version 4.4 appears to work on Windows Vista. Please report any problems.
Screen size should be at least 1024 x 768, but preferably 1280 x 1024

Density 4 is supplied as a single zip file.
No special installation is required.
Unzip (extract) all files to one folder
Create a shortcut to density4.exe

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Troubleshooting
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# I cannot open the help file. What is wrong?

Density4.chm is a compiled Windows help file, created with the Microsoft 
help compiler V 1.4. 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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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                        
15 01 2008 Build 4.1.2.17  Fixed bug in Trap Builder (Grids: enable numeric labels)
                           Fixed bug in IP: output value of IPInfrW no longer lost
                           Improvements
                           - ML SECR enabled for proximity detectors when there 
                             is just one sampling occasion (see Help ML SECR)
                           - Animal x site option added to Summary tab and View menu
                           - Auto ini values for proximity detectors use new RPSV algorithm

Release 4.1.3
08 04 2008 Build 4.1.3.1   Implemented modelling of known deaths during trapping in ML SECR multi-live model
                           (capture histories of dead animals are right-censored after the occasion of death)
                           The number not released NotRlsd is reported in the log when data are read.
                           (Usually these are animals that died in traps)
                           Fixed bug in display of captures x site summary table when some animals die in traps
                           Fixed other minor interface bugs 
			   Restored max capture records to 100000 in main (trial only)
                           PowerAnalysis
                           - Option for compound halfnormal detection fixed
                           - Export captures: suppress undocumented addition of error to distance covariate field

24 05 2008 Build 4.1.3.2
30 05 2008 Build 4.1.3.3   Minimum number of recaptures for ML SECR default setting changed to zero
                           (for analysis of 1-occasion data from proximity detectors; not appropriate for trapping)

01 08 2008 Build 4.1.4.1   Installed updated Delphi HTML Help kit, as possible fix for some Vista problems

Release 4.2.1
23 09 2008 Build 4.2.1.x   Compiled with new version number for update of website.

Release 4.2.2
05 10 2008 Build 4.2.2.3   Changes in this release affect only multi-session studies. 
                           When density is estimated by ML SECR with conditional likelihood 
                           (as a derived parameter) it is no longer assumed that all sessions 
                           use the same trap layout for the same number of occasions (now 
                           the effective sampling area 'esa' may vary between sessions). 
                           Full session labels are used more widely.
                           A popup menu option in the 'Trap layout' box allows a file list 
                           to be edited in a text box.
                           Minor improvements to Help file. 
14 10 2008 Build 4.2.2.5   Fixed bug find/replace in the text editor used when viewing log file etc.
                           Slight improvements to text editor: up/down search, prompt to save if modified.
                           Popup menu option to edit 'Trap layout' file list also implemented in PowerAnalysis.

Release 4.2.3
28 10 2008 Build 4.2.3.2   Allowed additive between-session covariate models in ML SECR. 
                           Revised ML SECR log output and labelling of beta parameters for ML SECR 
                           between-session models. Fixed bug in ML SECR that caused access violation
                           for session>1 when no between-session model, and enabled ML InfrW for 
                           between-session ML SECR models.
                           Suppress empty fields in output for ML hazard function shape parameter (z) 
                           when another detection function is used.
                           Mesh for 2D integration (ML SECR) optionally imported from text file.

Release 4.3.1
15 11 2008 Build 4.3.1.4   Fixed significant longstanding bug in mean maximum distance moved (MMDM) and
                           asymptotic range length (ARL) calculations.
                           Added some simulation capability for ETA.
26 11 2008 Build 4.3.1.5   Hide Options | ML SECR | Score tests (this is under construction and should 
                           not have been revealed in 4.3.1.4).
                           Minor changes to Help.
Release 4.3.2
08 01 2009 Build 4.3.2.1   Tweaked non-essential features: output of 'MLInfrW' is now correct when a 
                           between-sessions model is specified with varying trap layouts, and convex 
                           trapping areas are computed with greater precision.

Release 4.4.1
19 04 2009 Build 4.4.1.2   New feature: define detector usage for ML SECR occasion by occasion 
                           Fixed various bugs in handling of covariates for within-session ML SECR models.
                           Better reporting of within-session covariates in log file
                           Default Huggins model changed from 'Learned response' to 'None' (null model)
                           Huggins model now handles losses on capture
                           Counting of captures and recaptures is now more reliable and consistent (fixed bug with losses on capture)
                           Habitat mask changes take effect without 'Read data'
                           Fixed some simulation options (bimodal home ranges, random trap layouts)
20 04 2009 Build 4.4.1.3   Work around occasional 'access violation' in CAPTURE interface

Release 4.4.2
27 04 2009 Build 4.4.2.13  Improved handling of habitat masks and imported mesh files for multiple sessions
                           Mesh files now may be session-specific 
                           New viewer for imported meshes in Options | Computation
                           Enhanced viewer for habitat masks
                           'Tools | Export | Coordinates of mesh' optionally restricts by distance to nearest trap
                           Fixed bug that caused lockup in ML SECR with some datasets
28 04 2009 Build 4.4.2.15  Minor adjustments
13 08 2009                 Minor change to handling of multiple records on the same occasion(duplicates)

Release 4.4.3
05 10 2009 Build 4.4.3.1   Check input for identical repeats (same animal, occasion, detector) and reject
                           Block reporting of area and limits of imported masks (cause of some instability)
                           Fixed minor bug in RPSV algorithm (did not use recaptures of first animal)
Release 4.4.4
28 10 2009 Build 4.4.4.1   Fixed minor bug when calculating ML SECR AICc with sample size <= (np + 1)
Release 4.4.5
24 12 2009 Build 4.4.5.1   Increased maximum number of occasions to 150
		           New export options in popup menu for trap map in poweranalysis 
05 01 2010 Build 4.4.5.2   Options | Input increased maximum occasions in line with above
05 04 2010 Build 4.4.5.3   Adjustments to closed population estimators: 
                           - added constant to log likelihood for 2-point mixture & beta-binomial
                           - check for illconditioned frequencies in Burnham & Overton jackknife
Release 4.4.6
19 10 2010 Build 4.4.6.1   Fixed bug in PowerAnalysis (did not 'Vary traps' with 'Each session' option)
                           Fixed bug in likelihood of Pradel open population model   
                           Added constant to likelihood of 2-part mixture and beta binomial Mh models for consistency with other closed-population estimators.
                           Added check for ill-conditioned data in Mh jaccknife estimator


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

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

murray.efford@otago.ac.nz
