R Code for Mark Analysis

Documentation for package ‘RMark’ version 3.0.0

Help Pages

A B C D E F G I K L M N P R S T V W

-- A --

ABeginnersGuide	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

-- B --

Blackduck	Black duck known fate data
brownie	San Luis Valley mallard data
Burnham	Burnham Live-Dead Model

-- C --

cleanup	Removes unused MARK output files
coef.mark	MARK model beta parameters
collapseCH	Split/collapse capture histories
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
compute.Sn	Various utility functions
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

-- D --

deer	White-tailed deer double observer spotlight capture-recapture analysis
deltamethod.special	Compute delta method variance for sum, cumsum, prod and cumprod functions
Density	Density Estimation with Telemetry
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
Donovan.7	Exercise 7 example data
Donovan.8	Exercise 8 example data

-- E --

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)

-- F --

fill.covariates	Fill covariate entries in MARK design matrix with values
find.covariates	Find covariates in MARK design matrix
find.possible.transitions	Multi-state Transition Functions

-- G --

get.link	Compute sets of link values for real parameters
get.real	Extract or compute sets of real parameters

-- I --

IELogitNormalMR	Example of Immigration-Emigration LogitNormal Mark-Resight model
import.chdata	Import capture-recapture data sets from space or tab-delimited files
inverse.link	Inverse link functions (internal use)

-- K --

Killdeer nest survival example data

-- L --

larksparrow	Lark Sparrow
LASP	Lark Sparrow
load.model	Load external model
logitCI	Various utility functions
LogitNormalMR	Example of LogitNormal Mark-Resight model

-- M --

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.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_design.covariates	Merge time (occasion) and/or group specific covariates into design data
model.average	Compute model averaged estimates
model.average.default	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
MStruncate	Truncate capture histories for multi-state models
MS_popan	Convert Multistate data for POPAN-style abundance estimation

-- N --

nat.surv	Various utility functions
NicholsMSOccupancy	Multi-state occupancy example data
NSpeciesOcc	Multiple Species Occupancy

-- P --

Paradise_shelduck	Mulstistate Live-Dead Paradise Shelduck Data
PIMS	Display PIM for a parameter
PoissonMR	Example of Poisson Mark-Resight model
Poisson_twoMR	Example of Poisson Mark-Resight model
pop.est	Various utility functions
popan.derived	Computes some derived abundance estimates for POPAN models
popan.NGross	Computes some derived abundance estimates for POPAN models
popan.Nt	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
ps	Mulstistate Live-Dead Paradise Shelduck Data

-- R --

RDMultScalOcc	Multi-scale dynamic occupancy models in RMark
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
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
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

-- S --

salamander	Salamander occupancy data
search.output.files	Various utility functions
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.ch	Provides a summary for the capture histories
summary.mark	Summary of MARK model parameters and results
summary_ch	Provides a summary for the capture histories

-- T --

tailarea.t	Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
tailarea.z	Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
transition.pairs	Multi-state Transition Functions
TransitionMatrix	Multi-state Transition Functions

-- V --

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

-- W --

weta	Occupancy data for Mahoenui Giant Weta
Whatsnew	Summary of changes by version
wwdo.09	White-winged dove Jolly-Seber POPAN Analysis Details
wwdo.10	White-winged dove Jolly-Seber POPAN Analysis Details
wwdo.popan	White-winged dove Jolly-Seber POPAN Analysis Details