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 5.0.0 is the current version, with recent changes listed here. A recent version of R is required (>= 3.5.0). 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_5.0.0.zip 3804K << current Windows binary
secr_5.0.0.tar.gz 1083K << current source package

Distributed with package

secr-overview 5.0.0.pdf 158K << introduction
secr-datainput 5.0.0.pdf 103K << data formatting and input

General interest

secr-version4.pdf 75K << major changes 3 > 4
secr-manual 5.0.0.pdf 1018K << help pages secr 5.0.0
secr-tutorial.pdf 211K
secr-habitatmasks.pdf 312K
secr-spatialdata.pdf 73K
secr-models.pdf 85K
secr-troubleshooting.pdf 108K

Special topics

secr-densitysurfaces.pdf 234K
secr-finitemixtures.pdf 98K
secr-markresight.pdf 154K
secr-multisession.pdf 200K
secr-noneuclidean.pdf 175K
secr-parameterisations.pdf 91K
secr-polygondetectors.pdf 434K
secr-sound.pdf 104K
secr-telemetry.pdf 477K
secr-trend.pdf 76K
secr-varyingeffort.pdf 75K

Archived versions

Last updated: 07 October 2024