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 4.6.9 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.  Bug reports may also be raised as issues on GitHub.

The main features of secr are described in 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). ipsecr implements the 'simulation and inverse prediction' method for a subset of models from secr (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 need several other packages that can be downloaded from CRAN  (use Packages | Install package(s)... on the Windows GUI).                  

secr_4.6.9.zip 3696K            << current Windows binary
secr_4.6.9.tar.gz 1083K       << current source package   

Distributed with package                  

secr-overview 4.6.9.pdf 160K      << introduction
secr-datainput 4.6.9.pdf 103K     << data formatting and input

General interest

secr-version4.pdf 75K             
secr-manual 4.6.9.pdf 1003K       << help pages secr 4.6.9
secr-tutorial.pdf 208K             
secr-habitatmasks.pdf 310K   
secr-spatialdata.pdf 71K
secr-models.pdf 84K   
secr-troubleshooting.pdf 105K  

Special topics

secr-densitysurfaces.pdf 277K
secr-finitemixtures.pdf 95K
secr-markresight.pdf 152K
secr-multisession.pdf 200K     
secr-noneuclidean.pdf 172K
secr-parameterisations.pdf 89K
secr-polygondetectors.pdf 431K
secr-sound.pdf 101K
secr-telemetry.pdf 475K
secr-trend.pdf 66K
secr-varyingeffort.pdf 72K

Archived versions

Last updated: 04 July 2024

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