Man pages for RMark
R Code for Mark Analysis

ABeginnersGuideA beginners introduction and guide to RMark
add.design.dataAdd design data
adjust.parameter.countAdjust count of estimated parameters
adjust.valueAdjust over-dispersion scale or a result value such as...
BlackduckBlack duck known fate data
brownieSan Luis Valley mallard data
Burnham#' Burnham Live-Dead Model
cleanupRemoves unused MARK output files
coef.markMARK model beta parameters
collect.model.namesCollect names of MARK model objects from list of R objects...
collect.modelsCollect MARK models into a list and optionally construct a...
compute.design.dataCompute design data for a specific parameter in the MARK...
compute.linkCompute estimates of link values
compute.links.from.realsCompute link values from real parameters
compute.realCompute estimates of real parameters
convert.inpConvert MARK input file to RMark dataframe
convert.link.to.realConvert link values to real parameters
covariate.predictionsCompute estimates of real parameters for multiple covariate...
crdmsExample data for Closed Robust Design Multistrata
create.mark.mcmcCreate mcmc object for analysis with coda
create.model.listCreates a dataframe of all combinations of parameter...
deerWhite-tailed deer double observer spotlight capture-recapture...
deltamethod.specialCompute delta method variance for sum, cumsum, prod and...
deriv_inverse.linkDerivatives of inverse of link function (internal use)
dipperDipper capture-recapture data
Donovan.7Exercise 7 example data
Donovan.8Exercise 8 example data
edwards.eberhardtRabbit capture-recapture data
example.dataSimulated data from Cormack-Jolly-Seber model
export.chdataExport capture-history data to MARK .inp format
export.MARKExport data and models for import in MARK
export.modelExport output files for appending into MARK .dbf/.fpt format
extract.indicesVarious utility functions
extract.mark.outputExtract results from MARK output file (internal use)
fill.covariatesFill covariate entries in MARK design matrix with values
find.covariatesFind covariates in MARK design matrix
get.linkCompute sets of link values for real parameters
get.realExtract or compute sets of real parameters
IELogitNormalMRExample of Immigration-Emigration LogitNormal Mark-Resight...
import.chdataImport capture-recapture data sets from space or...
inverse.linkInverse link functions (internal use)
killdeerKilldeer nest survival example data
larksparrowLark Sparrow
load.modelLoad external model
LogitNormalMRExample of LogitNormal Mark-Resight model
make.design.dataCreate design dataframes for MARK model specification
make.mark.modelCreate a MARK model for analysis
make.time.factorMake time-varying dummy variables from time-varying factor...
mallardMallard nest survival example
markInterface to MARK for fitting capture-recapture models
mark.wrapperConstructs and runs a set of MARK models from a dataframe of...
mark.wrapper.parallelConstructs and runs in parallel a set of MARK models from a...
mata.waldModel-Averaged Tail Area Wald (MATA-Wald) confidence...
merge_design.covariatesMerge time (occasion) and/or group specific covariates into...
merge.markMerge mark model objects and lists of mark model objects
model.averageCompute model averaged estimates
model.average.listCompute model averaged estimates of real parameters from a...
model.average.marklistCompute model averaged estimates of real parameters
model.tableCreate table of MARK model selection results
MS_popanConvert Multistate data for POPAN-style abundance estimation
mstrataMultistrata example data
MStruncateTruncate capture histories for multi-state models
NicholsMSOccupancyMulti-state occupancy example data
PIMSDisplay PIM for a parameter
PoissonMRExample of Poisson Mark-Resight model
Poisson_twoMRExample of Poisson Mark-Resight model
popan.derivedComputes some derived abundance estimates for POPAN models
predict_realCompute estimates of real parameters with individual and...
print.markPrint MARK objects
print.marklistPrint MARK list objects
print.summary.markPrints summary of MARK model parameters and results
process.chProcess release-recapture history data
process.dataProcess encounter history dataframe for MARK analysis
RDOccupancyRobust Design occupancy example data
RDSalamanderRobust design salamander occupancy data
read.mark.binaryReads binary file output from MARK and returns a list of the...
release.gofRuns RELEASE for goodness of fit test
remove.markRemove mark models from list
rerun.markRuns a previous MARK model with new starting values
robustRobust design example data
run.mark.modelRuns analysis with MARK model using MARK.EXE
run.modelsRuns a set of MARK models
salamanderSalamander occupancy data
setup.modelDefines model specific parameters (internal use)
setup.parametersSetup parameter structure specific to model (internal use)
skagitAn example of the Mulstistrata (multi-state) model in which...
splitCHSplit/collapse capture histories
storeStore models externally or restore to workspace from external...
strip.commentsStrip comments
summary_chProvides a summary for the capture histories
summary.markSummary of MARK model parameters and results
TransitionMatrixMulti-state Transition Functions
valid.parametersDetermine validity of parameters for a model (internal use)
var.componentsVariance components estimation
var.components.remlVariance components estimation using REML or maximum...
wetaOccupancy data for Mahoenui Giant Weta
WhatsnewSummary of changes by version
wwdo.popanWhite-winged dove Jolly-Seber POPAN Analysis Details
RMark documentation built on Aug. 8, 2017, 5:08 p.m.