R package openCR

The R package openCR implements open-population capture-recapture models for data in the secr capthist format.

Features

  • spatial and nonspatial models
  • seamless integration with secr 
  • choice of parameterization, covering most earlier CJS and JS models
  • robust design
  • formulas for model specification 
  • open-source

Warnings

  • this software is new and may contain bugs (see Known bugs below)
  • users should be R-literate and familiar with capture-recapture
  • see openCR-vignette.pdf for a list of limitations and speed tips.

Known bugs (fixed in next release)

  • when the intervals between primary sessions are not 1.0, derived.openCR returns bad estimates for session-specific f, D and related parameters 
  • openCR.fit movement models are unreliable (underestimate phi, movement scale)
  • openCR.fit with JSSAsecrX models and count data with binomN = 0 (Poisson counts) provides erroneous estimates, particularly of lambda0 and sigma
  • predict.openCR fails when one parameter estimated (others fixed)
  • summary.openCR fails with non-spatial data (because secr::moves crashes out with non-spatial data, secr <= 3.2.0)

openCR is available from CRAN - including Windows and Mac binaries. Direct questions to the DENSITY|secr forum at phidot.org or the Google group secr.          

openCR_1.3.5.zip 1454K       << current Windows binary
openCR_1.3.5.tgz 1428K       << current OS X binary
openCR_1.3.5.tar.gz 468K     << current source package  

Distributed with package                  

openCR-vignette.pdf 229K      << introduction and overview
openCR-manual.pdf 247K       << help pages openCR 1.3.5

Additional vignettes

openCR-examples.pdf 235K   << examples 


Archived versions

Last updated: 13 April 2019

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