marked: Mark-Recapture Analysis for Survival and Abundance Estimation

Functions for fitting various models to capture-recapture data including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. Includes a CJS models that concurrently estimates and corrects for tag loss. Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty.

Version: 1.1.13
Depends: R (≥ 2.15.0), lme4, methods, parallel
Imports: graphics, stats, utils, R2admb, truncnorm, coda, Matrix, numDeriv, expm, Rcpp (≥ 0.9.13), TMB, optimx (≥ 2013.8.6)
LinkingTo: Rcpp
Suggests: ggplot2
Published: 2016-12-06
Author: Jeff Laake, Devin Johnson, Paul Conn
Maintainer: Jeff Laake <jefflaake at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
SystemRequirements: ADMB version 11 <> for use.admb=TRUE; see readme.txt
Citation: marked citation info
Materials: NEWS
In views: Environmetrics
CRAN checks: marked results


Reference manual: marked.pdf
Vignettes: Using marked
Package source: marked_1.1.13.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: marked_1.1.13.tgz
OS X Mavericks binaries: r-oldrel: marked_1.1.13.tgz
Old sources: marked archive

Reverse dependencies:

Reverse imports: RWildbook
Reverse suggests: FSA


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