R package secr

The R package secr has most of the features of DENSITY and many more. The R environment offers great advantages for advanced users, including the ability to control details of optimization, batch processing etc. For those less confident in R there is an interface that runs in a web browser.

secr 4.4.5 is the current version, with recent changes listed here. A recent version of R is required (>= 3.5.0). The code was substantially rewritten for secr 4.0 but the interface remains much the same. The changes between 3.2 and 4.2 are explained in secr-version4.pdf. Earlier versions are archived below. 

Corrections, bug reports and suggestions are welcome.  Please direct queries to the Google group secr or the DENSITY | secr forum at phidot.org

The features of DENSITY and secr 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_4.4.5.zip 4148K           << current Windows binary
secr_4.4.5.tar.gz 1062K      << current source package   

Distributed with package                  

secr-overview.pdf 171K      << introduction
secr-datainput.pdf 111K     << data formatting and input

General interest

secr-version4.pdf 75K             
secr-manual.pdf 932K         << help pages secr 4.4.5
secr-tutorial.pdf 221K             
secr-habitatmasks.pdf 333K   
secr-models.pdf 84K   
secr-troubleshooting.pdf 105K  

Special topics

secr-densitysurfaces.pdf 211K
secr-finitemixtures.pdf 100K
secr-markresight.pdf 155K
secr-multisession.pdf 202K     
secr-noneuclidean.pdf 211K
secr-parameterisations.pdf 89K
secr-polygondetectors.pdf 429K
secr-sound.pdf 104K
secr-telemetry.pdf 476K
secr-varyingeffort.pdf 75K

Archived versions

Last updated: 26 July 2021

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