Software for spatially explicit capture-recapture

Latest: secr 2.9.2 bug fix 2014-11-24

Use the Windows application DENSITY 5.0 or the R package secr to estimate the density or size of an animal population from capture-recapture data collected using an array of 'detectors'.  Detectors may be live-capture traps, with animals uniquely marked; they also may be sticky traps or snags that passively sample hair, from which individuals are distinguished by their DNA microsatellites, microphones, or cameras that take photographs from which individuals are recognized by their natural marks.  In secr it is possible also to analyse data obtained by searching areas for identifiable cues such as faeces (that is just one of many useful new features in secr). Both packages include tools for plotting and simulating spatial capture-recapture data, creating geometric arrays of detectors, etc.

Spatially explicit capture-recapture (SECR) uses the locations where each animal is detected to fit a spatial model of the detection process, and hence to obtain estimates of population density unbiased by edge effects and incomplete detection.  Inverse prediction (IP SECR) and maximum likelihood (ML SECR) are alternative methods for fitting the spatial detection model (Efford 2004, Borchers & Efford 2008).  See What is SECR? for more.

DENSITY runs under Windows XP and Windows 7, and possibly Windows 8 (it has not been tested).  Screen size should be set to at least 1024 x 768 pixels. Check the file readme5.txt for more information.  An online help file is included.  The software is free and no warranty is provided.  DENSITY 5.0, released December 2012, is the first new version for several years. It has much the same capabilities and interface as previous releases, but is generally cleaner. A bug has been fixed in the variance estimate for some conditional-likelihood (Horvitz-Thompson) density estimates. A batch R interface has been added as a bridge to 'secr', an R package that has many advanced features but lacks the graphical interface of DENSITY.  Specific changes and new features in 5.0 are listed here

In Density 5.0.3 (April 2014) a bug is fixed that could cause some points to be dropped from the computation mesh. The effect on estimates is expected to be minimal.

The R package secr covers a much wider range of analyses than DENSITY.  secr 2.9.1 is available on CRAN (a bug fix 2.9.2 is available here). Click here for a full list of changes

Please also note the DENSITY | secr forum at phidot.org (forum FAQ) and the Google group secr.

Download DENSITY 5.0 

Previous versions may also be accessed through this link.

Last Updated: 24 November 2014

University of Otago DENSITY: software for spatially explicit capture-recapture