Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
This package provides a framework for handling data and
analysis for mark-recapture.  Currently it is limited to
Cormack-Jolly-Seber and Jolly-Seber models.
R (>= 2.12.0), optimx, coda, truncnorm, Matrix, Rcpp (>=
0.9.13), ggplot2
ADMB version 11 (http://admb-project.org/) for
use.admb=TRUE; see readme.txt
'cjs.accumulate.R' 'cjs.initial.R' 'cjs.lnl.r' 'cjs.R'
'create.dm.R' 'create.dmdf.R' 'create.links.r' 'crm.R'
'fix.parameters.r' 'js.lnl.r' 'js.r' 'make.design.data.R'
'marked-package.R' 'merge.design.covariates.r' 'print.crm.r'
'process.ch.R' 'process.data.R' 'setup.model.R'
'setup.parameters.R' 'utility.R' 'valid.parameters.R' 'zzz.R'
'probitCJS.R' 'splitCH.R' 'cjs.hessian.r' 'extract.fcts.r'
'summary.fcts.R' 'crm.wrapper.R' 'js.hessian.R'
'js.accumulate.R' 'compute.real.R' 'convert.link.to.real.r'
'deriv.inverse.link.R' 'inverse.link.R' 'predict.crm.r'
'scale.r' 'set.initial.r' 'mscjs.r' 'mixed.model.r'
'proc.form.r'

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.
graphics, stats, utils, R2admb, truncnorm, coda, ggplot2,
Matrix, numDeriv, expm, Rcpp (>= 0.9.13), optimx (>= 2013.8.6)

graphics, stats, utils, R2admb, truncnorm, coda, Matrix,
numDeriv, expm, Rcpp (>= 0.9.13), optimx (>= 2013.8.6)

graphics, stats, utils, R2admb, truncnorm, coda, Matrix,
numDeriv, expm, Rcpp (>= 0.9.13), TMB, optimx (>= 2013.8.6)
ADMB version 11 <http://admb-project.org/> for
use.admb=TRUE; see readme.txt

R2admb, truncnorm, coda, optimx (>= 2013.8.6), ggplot2,
Matrix, numDeriv, Rcpp (>= 0.9.13)