ABeginnersGuide         A beginners introduction and guide to RMark
Blackduck               Black duck known fate data
Burnham                 Burnham Live-Dead Model
Density                 Density Estimation with Telemetry
Donovan.7               Exercise 7 example data
Donovan.8               Exercise 8 example data
HidMarkov               Hidden Markov Model
IELogitNormalMR         Example of Immigration-Emigration LogitNormal
                        Mark-Resight model
LogitNormalMR           Example of LogitNormal Mark-Resight model
MSJollySeber            Multistate Jolly Seber
MS_popan                Convert Multistate data for POPAN-style
                        abundance estimation
MStruncate              Truncate capture histories for multi-state
                        models
NSpeciesOcc             Multiple Species Occupancy
NicholsMSOccupancy      Multi-state occupancy example data
PIMS                    Display PIM for a parameter
Paradise_shelduck       Mulstistate Live-Dead Paradise Shelduck Data
PoissonMR               Example of Poisson Mark-Resight model
Poisson_twoMR           Example of Poisson Mark-Resight model
RDMultScalOcc           Multi-scale dynamic occupancy models in RMark
RDOccupancy             Robust Design occupancy example data
RDSalamander            Robust design salamander occupancy data
TransitionMatrix        Multi-state Transition Functions
Whatsnew                Summary of changes by version
add.design.data         Add design data
adjust.parameter.count
                        Adjust count of estimated parameters
adjust.value            Adjust over-dispersion scale or a result value
                        such as effective sample size
brownie                 San Luis Valley mallard data
cleanup                 Removes unused MARK output files
coef.mark               MARK model beta parameters
collect.model.names     Collect names of MARK model objects from list
                        of R objects (internal function)
collect.models          Collect MARK models into a list and optionally
                        construct a table of model results
compute.design.data     Compute design data for a specific parameter in
                        the MARK model (internal use)
compute.link            Compute estimates of link values
compute.links.from.reals
                        Compute link values from real parameters
compute.real            Compute estimates of real parameters
convert.inp             Convert MARK input file to RMark dataframe
convert.link.to.real    Convert link values to real parameters
covariate.predictions   Compute estimates of real parameters for
                        multiple covariate values
crdms                   Example data for Closed Robust Design
                        Multistrata
create.mark.mcmc        Create mcmc object for analysis with coda
create.model.list       Creates a dataframe of all combinations of
                        parameter specifications
deer                    White-tailed deer double observer spotlight
                        capture-recapture analysis
deltamethod.special     Compute delta method variance for sum, cumsum,
                        prod and cumprod functions
deriv_inverse.link      Derivatives of inverse of link function
                        (internal use)
dipper                  Dipper capture-recapture data
edwards.eberhardt       Rabbit capture-recapture data
example.data            Simulated data from Cormack-Jolly-Seber model
export.MARK             Export data and models for import in MARK
export.chdata           Export capture-history data to MARK .inp format
export.model            Export output files for appending into MARK
                        .dbf/.fpt format
extract.indices         Various utility functions
extract.mark.output     Extract results from MARK output file (internal
                        use)
fill.covariates         Fill covariate entries in MARK design matrix
                        with values
find.covariates         Find covariates in MARK design matrix
get.link                Compute sets of link values for real parameters
get.real                Extract or compute sets of real parameters
import.chdata           Import capture-recapture data sets from space
                        or tab-delimited files
inverse.link            Inverse link functions (internal use)
killdeer                Killdeer nest survival example data
larksparrow             Lark Sparrow
load.model              Load external model
make.design.data        Create design dataframes for MARK model
                        specification
make.mark.model         Create a MARK model for analysis
make.time.factor        Make time-varying dummy variables from
                        time-varying factor variable
mallard                 Mallard nest survival example
mark                    Interface to MARK for fitting capture-recapture
                        models
mark.wrapper            Constructs and runs a set of MARK models from a
                        dataframe of parameter specifications
mark.wrapper.parallel   Constructs and runs in parallel a set of MARK
                        models from a dataframe of parameter
                        specifications
mata.wald               Model-Averaged Tail Area Wald (MATA-Wald)
                        confidence intervals
merge.mark              Merge mark model objects and lists of mark
                        model objects
merge_design.covariates
                        Merge time (occasion) and/or group specific
                        covariates into design data
model.average           Compute model averaged estimates
model.average.list      Compute model averaged estimates of real
                        parameters from a list structure for estimates
model.average.marklist
                        Compute model averaged estimates of real
                        parameters
model.table             Create table of MARK model selection results
mstrata                 Multistrata example data
popan.derived           Computes some derived abundance estimates for
                        POPAN models
predict_real            Compute estimates of real parameters with
                        individual and design covariates
print.mark              Print MARK objects
print.marklist          Print MARK list objects
print.summary.mark      Prints summary of MARK model parameters and
                        results
process.ch              Process release-recapture history data
process.data            Process encounter history dataframe for MARK
                        analysis
readMarkVcv             Reads binary file output from MARK and returns
                        a list of the results
release.gof             Runs RELEASE for goodness of fit test
remove.mark             Remove mark models from list
rerun.mark              Runs a previous MARK model with new starting
                        values
robust                  Robust design example data
run.mark.model          Runs analysis with MARK model using MARK.EXE
run.models              Runs a set of MARK models
salamander              Salamander occupancy data
setup.model             Defines model specific parameters (internal
                        use)
setup.parameters        Setup parameter structure specific to model
                        (internal use)
skagit                  An example of the Multistrata (multi-state)
                        model in which states are routes taken by
                        migrating fish.
splitCH                 Split/collapse capture histories
store                   Store models externally or restore to workspace
                        from external storage
strip.comments          Strip comments
summary.mark            Summary of MARK model parameters and results
summary_ch              Provides a summary for the capture histories
valid.parameters        Determine validity of parameters for a model
                        (internal use)
var.components          Variance components estimation
var.components.reml     Variance components estimation using REML or
                        maximum likelihood
weta                    Occupancy data for Mahoenui Giant Weta
wwdo.popan              White-winged dove Jolly-Seber POPAN Analysis
                        Details
