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.

AuthorJeff Laake <jeff.laake@noaa.gov>, Devin Johnson <devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Date of publication2016-12-06 18:27:17
MaintainerJeff Laake <jefflaake@gmail.com>
LicenseGPL (>= 2)
Version1.1.13

View on CRAN

Man pages

backward_prob: Computes backward probabilities

cjs: Fitting function for CJS models

cjs.accumulate: Accumulates common capture history values

cjs_delta: HMM Initial state distribution functions

cjs_gamma: HMM Transition matrix functions

cjs.hessian: Compute variance-covariance matrix for fitted CJS model

cjs.initial: Computes starting values for CJS p and Phi parameters

cjs.lnl: Likelihood function for Cormack-Jolly-Seber model

cjs_tmb: Fitting function for CJS models

coef.crm: Extract coefficients

compute_matrices: Compute HMM matrices

compute.real: Compute estimates of real parameters

convert.link.to.real: Convert link values to real parameters

create.dm: Creates a design matrix for a parameter

create.dmdf: Creates a dataframe with all the design data for a particular...

create.fixed.matrix: Create parameters with fixed matrix

create.links: Creates a 0/1 vector for real parameters with sin link

crm: Capture-recapture model fitting function

crm.wrapper: Automation of model runs

deriv_inverse.link: Derivatives of inverse of link function (internal use)

dipper: Dipper capture-recapture data

dmat_hsmm2hmm: Create expanded state-dependent observation matrix for HMM...

fix.parameters: Fixing real parameters in crm models

function.wrapper: Utility extract functions

global_decode: Global decoding of HMM

hmmDemo: HMM computation demo functions

HMMLikelihood: Hidden Markov Model likelihood functions

hsmm2hmm: Compute transition matrix for HMM from HSMM

initiate_pi: Setup fixed values for pi in design data

inverse.link: Inverse link functions (internal use)

js: Fitting function for Jolly-Seber model using Schwarz-Arnason...

js.accumulate: Accumulates common capture history values

js.hessian: Compute variance-covariance matrix for fitted JS model

js.lnl: Likelihood function for Jolly-Seber model using...

local_decode: Local decoding of HMM

make.design.data: Create design dataframes for crm

merge_design.covariates: Merge time (occasion) and/or group specific covariates into...

mixed.model.admb: Mixed effect model contstruction

mscjs: Fitting function for Multistate CJS models

mstrata: Multistrata example data

mvmscjs: Fitting function for Multivariate Multistate CJS with...

mvms_design_data: Multivariate Multistate (mvms) Design Data

mvms_dmat: HMM Observation Probability matrix functions

omega: Compute 1 to k-step transition proportions

Phi.mean: Various utility parameter summary functions

predict.crm: Compute estimates of real parameters

print.crm: Print model results

print.crmlist: Print model table from model list

probitCJS: Perform MCMC analysis of a CJS model

process.ch: Process release-recapture history data

process.data: Process encounter history dataframe for MARK analysis

proc.form: Mixed effect model formula parser Parses a mixed effect model...

resight.matrix: Various utility functions

R_HMMLikelihood: Hidden Markov Model Functions

sealions: Multivariate State example data

set.fixed: Set fixed real parameter values in ddl

set.initial: Set initial values

set_mvms: Multivariate Multistate (mvms) Specification

set.scale: Scaling functions

setup_admb: ADMB setup

setup.model: Defines model specific parameters (internal use)

setup.parameters: Setup parameter structure specific to model (internal use)

setup_tmb: TMB setup

simHMM: Simulates data from Hidden Markov Model

skagit: An example of the Mulstistrata (multi-state) model in which...

splitCH: Split/collapse capture histories

tagloss: Tag loss example

valid.parameters: Determine validity of parameters for a model (internal use)

Files in this package

marked
marked/inst
marked/inst/cjsre_tmb.cpp
marked/inst/parameters.txt
marked/inst/CITATION
marked/inst/cjsre.tpl
marked/inst/models.txt
marked/inst/mvms.tpl
marked/inst/cjs_tmb.cpp
marked/inst/xmodelm5.cpp
marked/inst/multistate.tpl
marked/inst/cjs_reml.tpl
marked/inst/df1b2gh.cpp
marked/inst/README.txt
marked/inst/df1b2ghmult.cpp
marked/inst/doc
marked/inst/doc/markedVignette.Rnw
marked/inst/doc/markedVignette.pdf
marked/inst/doc/markedVignette.R
marked/inst/minfil.cpp
marked/inst/cjs.tpl
marked/src
marked/src/cjs2tlgam.f
marked/src/Makevars
marked/src/bayesCR.cpp
marked/src/ms2gamma.f
marked/src/hmm_like.f
marked/src/cjsdmat.f
marked/src/cjs2tldmat.f
marked/src/cjs1tldmat.f
marked/src/mvmsdmat.f
marked/src/cjs1tlgam.f
marked/src/msdmat.f
marked/src/Makevars.win
marked/src/umsdmat.f
marked/src/cjsgamma.f
marked/src/ums2dmat.f
marked/src/cjs.f
marked/src/msgamma.f
marked/NAMESPACE
marked/demo
marked/demo/00Index
marked/demo/tests.r
marked/NEWS
marked/data
marked/data/mstrata.rda
marked/data/dipper.rda
marked/data/skagit.rda
marked/data/tagloss.rda
marked/data/sealions.rda
marked/R
marked/R/mixed.model.r
marked/R/predict.crm.r
marked/R/admbutils.R
marked/R/proc.formula.r
marked/R/js.r
marked/R/js.accumulate.R
marked/R/js.lnl.r
marked/R/compute.real.R
marked/R/RHMMLikelihood.r
marked/R/print.crm.r
marked/R/cjs.lnl.r
marked/R/setup.parameters.R
marked/R/convert.link.to.real.r
marked/R/create.links.r
marked/R/Observation_functions.r
marked/R/mscjs.r
marked/R/set.initial.r
marked/R/create.dmdf.R marked/R/crm.wrapper.R marked/R/summary.fcts.R
marked/R/cjs.hessian.r
marked/R/process.data.R marked/R/js.hessian.R
marked/R/Transition_functions.r
marked/R/setup.model.R marked/R/splitCH.R marked/R/probitCJS.R marked/R/utility.R marked/R/valid.parameters.R marked/R/cjs.initial.R
marked/R/extract.fcts.r
marked/R/cjs.accumulate.R marked/R/inverse.link.R
marked/R/fix.parameters.r
marked/R/simplify.r
marked/R/make.design.data.R
marked/R/InitialDistribution_functions.r
marked/R/set.fixed.R
marked/R/hsmm2hmm.r
marked/R/scale.r
marked/R/HMMLikelihood.r
marked/R/cjs.R marked/R/cjs_tmb.R
marked/R/HMMutilities.r
marked/R/crm.R
marked/R/simHMM.r
marked/R/create.dm.R
marked/R/hmmDemo.r
marked/R/set_mvms.r
marked/R/deriv.inverse.link.R marked/R/process.ch.R
marked/R/merge.design.covariates.r
marked/R/omega.r
marked/R/marked-package.R
marked/R/coef.r
marked/R/mvmscjs.R marked/R/zzz.R
marked/vignettes
marked/vignettes/markedVignette.Rnw
marked/vignettes/markedWriteUpBib.bib
marked/MD5
marked/build
marked/build/vignette.rds
marked/DESCRIPTION
marked/man
marked/man/merge_design.covariates.Rd marked/man/hmmDemo.Rd marked/man/valid.parameters.Rd marked/man/compute_matrices.Rd marked/man/function.wrapper.Rd marked/man/process.data.Rd marked/man/set_mvms.Rd marked/man/cjs_delta.Rd marked/man/process.ch.Rd marked/man/mstrata.Rd marked/man/mvms_design_data.Rd marked/man/backward_prob.Rd marked/man/local_decode.Rd marked/man/hsmm2hmm.Rd marked/man/setup.model.Rd marked/man/probitCJS.Rd marked/man/tagloss.Rd marked/man/inverse.link.Rd marked/man/cjs_tmb.Rd marked/man/js.hessian.Rd marked/man/mvmscjs.Rd marked/man/create.dm.Rd marked/man/deriv_inverse.link.Rd marked/man/set.scale.Rd marked/man/global_decode.Rd marked/man/js.accumulate.Rd marked/man/HMMLikelihood.Rd marked/man/create.links.Rd marked/man/predict.crm.Rd marked/man/cjs.accumulate.Rd marked/man/dmat_hsmm2hmm.Rd marked/man/compute.real.Rd marked/man/proc.form.Rd marked/man/skagit.Rd marked/man/make.design.data.Rd marked/man/omega.Rd marked/man/convert.link.to.real.Rd marked/man/mvms_dmat.Rd marked/man/create.dmdf.Rd marked/man/setup.parameters.Rd marked/man/resight.matrix.Rd marked/man/print.crmlist.Rd marked/man/cjs.Rd marked/man/create.fixed.matrix.Rd marked/man/set.initial.Rd marked/man/setup_tmb.Rd marked/man/simHMM.Rd marked/man/set.fixed.Rd marked/man/cjs.lnl.Rd marked/man/js.Rd marked/man/cjs.initial.Rd marked/man/splitCH.Rd marked/man/sealions.Rd marked/man/js.lnl.Rd marked/man/R_HMMLikelihood.Rd marked/man/cjs.hessian.Rd marked/man/mixed.model.admb.Rd marked/man/crm.wrapper.Rd marked/man/cjs_gamma.Rd marked/man/fix.parameters.Rd marked/man/Phi.mean.Rd marked/man/coef.crm.Rd marked/man/mscjs.Rd marked/man/setup_admb.Rd marked/man/dipper.Rd marked/man/crm.Rd marked/man/initiate_pi.Rd marked/man/print.crm.Rd

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