R package secr

The R package secr has most of the features of DENSITY and major new ones:

  • modelling of density surfaces (inhomogeneous Poisson distribution of home ranges)
  • flexible formula-based model specification
  • model averaging
  • area search ('polygon') and route search ('transect') detectors
  • acoustic detection
  • parallel processing (some functions)
  • hybrid mixture models (hcov)
  • a0 parameterization for compensatory heterogeneity
  • telemetry integrated with capture-recapture
  • regression spline smooths based on mgcv
  • user-provided non-Euclidean distances
  • mark-resight models 

The R environment offers great advantages for advanced users, including the ability to control details of optimization, batch processing etc. 

secr 3.1.8 is the current version; recent changes are listed here. Earlier versions are archived below.  Major changes were made between secr 2.10 and secr 3.0 (see NEWS). Corrections, bug reports and documentation suggestions are welcome.

Please direct queries to the Google group secr or the DENSITY | secr forum at phidot.org (forum FAQ). 

The features of DENSITY and secr 3.1 are compared in an appendix of the overview pdf (below). The package secrdesign provides tools for study design. secrlinear is an add-on to secr for animals in linear habitats such as river systems (vignette). openCR performs open-population analyses (vignette).

secr is available from CRAN - including Windows and Mac binaries - so you should not need to download from here. Just follow your usual route for installing packages from your R GUI (e.g., Packages | Install package(s) in Windows). See below for various pieces of documentation including an overview of secr and a pdf version of the help pages.

In Windows you can also install secr by saving the binary zip file (below) to a local folder and using the menu option "Packages | Install packages(s) from local zip files...".  Then remember to load it!  You will also need the packages abind, sp, stringr and raster, and possibly maptools, spsurveyrgdalrgeos and others (use Packages | Install package(s)... to download from CRAN).                  

secr_3.1.8.zip 3681K           << current Windows binary
secr_3.1.8.tar.gz 1191K      << current source package  

Distributed with package                  

secr-overview.pdf 167K      << introduction
secr-datainput.pdf 110K     << data formatting and input secr 3.1.8

General interest

secr-manual.pdf 860K         << help pages secr 3.1.8
secr-tutorial.pdf 221K             
secr-habitatmasks.pdf 332K   
secr-models.pdf 85K   
secr-troubleshooting.pdf 99K  

Special topics

secr-densitysurfaces.pdf 201K
secr-finitemixtures.pdf 100K
secr-markresight.pdf 151K
secr-multisession.pdf 199K     
secr-noneuclidean.pdf 211K
secr-parameterisations.pdf 89K
secr-polygondetectors.pdf 434K
secr-sound.pdf 100K
secr-telemetry.pdf 534K
secr-varyingeffort.pdf 73K

Archived versions

Last updated: 13 December 2018

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