R Code for mark-recapture analysis


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Documentation for package ‘marked’ version 1.1.3

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accumulate_data Process encounter history dataframe for MARK analysis
backward_prob Hidden Markov Functions
cjs Fitting function for CJS models
cjs.accumulate Accumulates common capture history values
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_delta HMM Initial state distribution functions
cjs_dmat HMM Observation Probability matrix functions
cjs_gamma HMM Transition matrix functions
coef.crm Print model results or extract coefficients
collapseCH Split/collapse capture histories
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 parameter in a crm model
create.dml Creates a design matrix for a parameter
create.fixed.matrix Create parameters with fixed matrix
create.links Creates a 0/1 vector for real parameters with sin link
create.model.list Automation of model runs
crm Capture-recapture model fitting function
crm.wrapper Automation of model runs
deriv.inverse.link Derivatives of inverse of link function (internal use)
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
fx.aic Utility extract functions
fx.par.count Utility extract functions
hmm.lnl Hidden Markov Model likelihood functions
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 POPAN formulation
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 Schwarz-Arnason POPAN formulation
load.model Automation of model runs
loglikelihood Hidden Markov Functions
make.design.data Create design dataframes for crm
mcmc_mode Various utility functions
merge.design.covariates Merge time (occasion) and/or group specific covariates into design data
merge_design.covariates Merge time (occasion) and/or group specific covariates into design data
mixed.model Mixed effect model contstruction
mixed.model.admb Mixed effect model contstruction
mixed.model.dat Mixed effect model contstruction
model.table Automation of model runs
ms2_gamma HMM Transition matrix functions
mscjs Fitting function for Multistate CJS models
ms_dmat HMM Observation Probability matrix functions
ms_gamma HMM Transition matrix functions
naive.survival Various utility functions
p.boxplot Various utility parameter summary functions
p.mean Various utility parameter summary functions
Phi.boxplot Various utility parameter summary functions
Phi.mean Various utility parameter summary functions
predict.crm Compute estimates of real parameters
print.crm Print model results or extract coefficients
print.crmlist Print model results or extract coefficients
probitCJS Perform MCMC analysis of a CJS model
probitMsCJS Perform MCMC analysis of a CJS model
proc.form Mixed effect model formula parser
process.ch Process release-recapture history data
process.data Process encounter history dataframe for MARK analysis
reals Hidden Markov Model likelihood functions
reindex Mixed effect model contstruction
resight.matrix Various utility functions
R_HMMLikelihood Hidden Markov Functions
scale.dm Scaling functions
scale.par Scaling functions
set.fixed Set fixed real parameter values in ddl
set.initial Set initial values
set.scale Scaling functions
setup.model Defines model specific parameters (internal use)
setup.parameters Setup parameter structure specific to model (internal use)
setupHMM Defines model specific parameters (internal use)
simHMM Simulates data from Hidden Markov Model
splitCH Split/collapse capture histories
ums2_dmat HMM Observation Probability matrix functions
ums_dmat HMM Observation Probability matrix functions
unscale.par Scaling functions
valid.parameters Determine validity of parameters for a model (internal use)