R Code for MARK Analysis

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Documentation for package ‘RMark’ version 1.9.4

Help Pages

A beginners guide A beginners introduction and guide to RMark
add.design.data Add design data
adjust.chat Adjust over-dispersion scale or a result value such as effective sample size
adjust.parameter.count Adjust count of estimated parameters
adjust.value Adjust over-dispersion scale or a result value such as effective sample size
Blackduck Black duck known fate data
cjs Fitting function for CJS models
cjs.lnl Likelihood function for Cormack-Jolly-Seber model
cleanup Removes unused MARK output files
coef.mark Summary of MARK model parameters and results
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
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.model.list Creates a dataframe of all combinations of parameter specifications
crm Capture-recapture model fitting function
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
Donovan.7 Exercise 7 example data
Donovan.8 Exercise 8 example data
edwards.eberhardt Rabbit capture-recapture data
example.data Simulated data from Cormack-Jolly-Seber model
export.chdata Export capture-history data to MARK .inp format
export.MARK Export data and models for import in MARK
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)
js Fitting function for Jolly-Seber model using Schwarz-Arnason POPAN formulation
js.lnl Likelihood function for Jolly-Seber model using Schwarz-Arnason POPAN formulation
killdeer Killdeer nest survival example data
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
merge.design.covariates Merge time (occasion) and/or group specific covariates into design data
merge.mark Merge mark model objects and lists of mark model objects
merge.occasion.data Merge occasion-specific covariate data 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
nat.surv Various utility functions
NicholsMSOccupancy Multi-state occupancy example data
PIMS Display PIM for a parameter
pop.est Various utility functions
popan.derived Computes some derived abundance estimates for POPAN models
popan.Nt Computes some derived abundance estimates for POPAN models
print.mark Print MARK objects
print.marklist Print MARK objects
print.summary.mark Summary of MARK model parameters and results
process.ch Process release-recapture history data
process.data Process encounter history dataframe for MARK analysis
RDOccupancy Robust Design occupancy example data
RDSalamander Robust design salamander occupancy data
read.mark.binary 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
restore Store models externally or restore to workspace from external storage
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)
store Store models externally or restore to workspace from external storage
summary.ch Provides a summary for the capture histories
summary.mark Summary of MARK model parameters and results
TransitionMatrix Creates a transition matrix of movement parameters for a multi-state(strata) model
valid.parameters Determine validity of parameters for a model (internal use)
var.components Variance components estimation
weta Occupancy data for Mahoenui Giant Weta
What's new Summary of changes by version