SECR in R

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 3.1.0 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, also available from CRAN, makes it easy to simulate different study designs and summarise the resulting estimates (vignette). secrlinear is an add-on to secr for animals in linear habitats such as river systems (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 and raster, and possibly maptools, spsurveyrgdal, and rgeos (use Packages | Install package(s)... to download from CRAN).                  

secr_3.1.0.zip 3575K           << current Windows binary
secr_3.1.0.tar.gz 2052K      << current source package  

Distributed with package                  

secr-overview.pdf 183K      << introduction
secr-manual.pdf 863K         << help pages secr 3.1.0
secr-datainput.pdf 112K     << data formatting and input secr 3.1.0

General interest

secr-tutorial.pdf 221K             << new 2017-04-08
secr-habitatmasks.pdf 332K   << new 2017-04-04
secr-troubleshooting.pdf 98K  << new 2017-04-08

Special topics (all revised April 2017)

secr-densitysurfaces.pdf 200K
secr-finitemixtures.pdf 100K
secr-markresight.pdf 151K
secr-multisession.pdf 192K     << new 2017-04-04
secr-noneuclidean.pdf 209K
secr-parameterisations.pdf 107K
secr-polygondetectors.pdf 441K
secr-sound.pdf 100K
secr-telemetry.pdf 534K
secr-varyingeffort.pdf 72K

Archived versions

Last updated: 22 September 2017

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