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.

Author
Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson <devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Date of publication
2016-03-07 22:31:49
Maintainer
Jeff Laake <Jeff.Laake@noaa.gov>
License
GPL (>= 2)
Version
1.1.11

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
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
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
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
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.model
Defines model specific parameters (internal use)
setup.parameters
Setup parameter structure specific to model (internal use)
simHMM
Simulates data from Hidden Markov Model
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/parameters.txt
marked/inst/CITATION
marked/inst/cjsre.tpl
marked/inst/models.txt
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/tagloss.rda
marked/data/sealions.rda
marked/R
marked/R/mixed.model.r
marked/R/predict.crm.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/scale.r
marked/R/HMMLikelihood.r
marked/R/cjs.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/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/setup.model.Rd
marked/man/probitCJS.Rd
marked/man/tagloss.Rd
marked/man/inverse.link.Rd
marked/man/js.hessian.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/compute.real.Rd
marked/man/proc.form.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/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/dipper.Rd
marked/man/crm.Rd
marked/man/print.crm.Rd