Software for spatially explicit capture-recapture

Latest: pre-release secr 4.2.3 2020-05-16

Use the R package secr or its older sibling, the Windows application DENSITY 5.0, 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 on recent versions of Windows.  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 has not changed since April 2014.  Its features are listed here

The R package secr covers a much wider range of analyses than DENSITY.  Version secr 4.2.2 is provided here and on CRAN. Changes are described in secr-version4.pdf. See secr 4.2.2 for bug fixes and some new features. The package secrdesign offers tools for simulation and study design, and you really should check out secrdesignapp.

The R package openCR offers both nonspatial and spatial open population analyses.

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

Download DENSITY 5.0 

Previous versions may also be accessed through this link.

Last updated: 16 May 2020

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