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)

Functions

accumulate_data Man page
backward_prob Man page
cjs Man page
cjs.accumulate Man page
cjs_delta Man page
cjs_dmat Man page
cjs_gamma Man page
cjs.hessian Man page
cjs.initial Man page
cjs.lnl Man page
cjs_tmb Man page
coef.crm Man page
collapseCH Man page
compute_matrices Man page
compute.real Man page
convert.link.to.real Man page
create.dm Man page
create.dmdf Man page
create.dml Man page
create.fixed.matrix Man page
create.links Man page
create.model.list Man page
crm Man page
crmlist_fromfiles Man page
crm.wrapper Man page
deriv_inverse.link Man page
deriv.inverse.link Man page
dipper Man page
dmat_hsmm2hmm Man page
fix.parameters Man page
function.wrapper Man page
fx.aic Man page
fx.par.count Man page
global_decode Man page
hmmDemo Man page
HMMLikelihood Man page
hmm.lnl Man page
hsmm2hmm Man page
initiate_pi Man page
inverse.link Man page
js Man page
js.accumulate Man page
js.hessian Man page
js.lnl Man page
load.model Man page
local_decode Man page
loglikelihood Man page
make.design.data Man page
mcmc_mode Man page
merge_design.covariates Man page
merge.design.covariates Man page
mixed.model Man page
mixed.model.admb Man page
mixed.model.dat Man page
model.table Man page
ms2_gamma Man page
mscjs Man page
ms_dmat Man page
ms_gamma Man page
mstrata Man page
mvmscjs Man page
mvmscjs_delta Man page
mvms_design_data Man page
mvms_dmat Man page
naive.survival Man page
omega Man page
p.boxplot Man page
Phi.boxplot Man page
Phi.mean Man page
p.mean Man page
predict.crm Man page
print.crm Man page
print.crmlist Man page
probitCJS Man page
process.ch Man page
process.data Man page
proc.form Man page
reals Man page
reindex Man page
rerun_crm Man page
resight.matrix Man page
R_HMMLikelihood Man page
scale.dm Man page
scale.par Man page
sealions Man page
set.fixed Man page
set.initial Man page
set_mvms Man page
set.scale Man page
setup_admb Man page
setupHMM Man page
setup.model Man page
setup.parameters Man page
setup_tmb Man page
simHMM Man page
skagit Man page
splitCH Man page
tagloss Man page
ums2_dmat Man page
ums_dmat Man page
unscale.par Man page
valid.parameters Man page

Files

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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