{
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"Date": "2026-06-12",
"Title": "R Code for Mark Analysis",
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"Description": "An interface to the software package MARK that constructs\ninput files for MARK and extracts the output. MARK was\ndeveloped by Gary White and is freely available at\n but is not\nopen source.",
"SystemRequirements": "notepad.exe, mark32.exe or mark64.exe on Windows\nand only mark on Linux (>= 11.2) (see README.txt in package\ndirectory)",
"URL": "https://github.com/jlaake/RMark/RMark",
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"adjust.value",
"cleanup",
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"collapseCH",
"collect.model.names",
"collect.models",
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"export.chdata",
"export.MARK",
"export.model",
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"get.real",
"import.chdata",
"logitCI",
"make.design.data",
"make.mark.model",
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"mark",
"mark.wrapper",
"mark.wrapper.parallel",
"mata.wald",
"merge_design.covariates",
"merge.mark",
"model.average",
"model.table",
"MS_popan",
"MStruncate",
"nat.surv",
"PIMS",
"pop.est",
"popan.derived",
"predict_real",
"print.marklist",
"print.summary.mark",
"process.ch",
"process.data",
"readMarkVcv",
"release.gof",
"remove.mark",
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"restore",
"run.mark.model",
"run.models",
"search.output.files",
"setup.model",
"setup.parameters",
"splitCH",
"store",
"summary_ch",
"summary.mark",
"transition.pairs",
"TransitionMatrix",
"var.components",
"var.components.reml"
],
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{
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{
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{
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{
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{
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{
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{
"page": "ABeginnersGuide",
"title": "A beginners introduction and guide to RMark",
"topics": [
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]
},
{
"page": "add.design.data",
"title": "Add design data",
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},
{
"page": "adjust.parameter.count",
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{
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{
"page": "Blackduck",
"title": "Black duck known fate data",
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{
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"title": "San Luis Valley mallard data",
"topics": [
"brownie"
]
},
{
"page": "Burnham",
"title": "Burnham Live-Dead Model",
"topics": [
"Burnham"
]
},
{
"page": "cleanup",
"title": "Removes unused MARK output files",
"topics": [
"cleanup"
]
},
{
"page": "coef.mark",
"title": "MARK model beta parameters",
"topics": [
"coef.mark"
]
},
{
"page": "collect.model.names",
"title": "Collect names of MARK model objects from list of R objects (internal function)",
"topics": [
"collect.model.names"
]
},
{
"page": "collect.models",
"title": "Collect MARK models into a list and optionally construct a table of model results",
"topics": [
"collect.models"
]
},
{
"page": "compute.design.data",
"title": "Compute design data for a specific parameter in the MARK model (internal use)",
"topics": [
"compute.design.data"
]
},
{
"page": "compute.link",
"title": "Compute estimates of link values",
"topics": [
"compute.link"
]
},
{
"page": "compute.links.from.reals",
"title": "Compute link values from real parameters",
"topics": [
"compute.links.from.reals"
]
},
{
"page": "compute.real",
"title": "Compute estimates of real parameters",
"topics": [
"compute.real"
]
},
{
"page": "convert.inp",
"title": "Convert MARK input file to RMark dataframe",
"topics": [
"convert.inp"
]
},
{
"page": "convert.link.to.real",
"title": "Convert link values to real parameters",
"topics": [
"convert.link.to.real"
]
},
{
"page": "covariate.predictions",
"title": "Compute estimates of real parameters for multiple covariate values",
"topics": [
"covariate.predictions"
]
},
{
"page": "crdms",
"title": "Example data for Closed Robust Design Multistrata",
"topics": [
"crdms"
]
},
{
"page": "create.mark.mcmc",
"title": "Create mcmc object for analysis with coda",
"topics": [
"create.mark.mcmc"
]
},
{
"page": "create.model.list",
"title": "Creates a dataframe of all combinations of parameter specifications",
"topics": [
"create.model.list"
]
},
{
"page": "deer",
"title": "White-tailed deer double observer spotlight capture-recapture analysis",
"topics": [
"deer"
]
},
{
"page": "deltamethod.special",
"title": "Compute delta method variance for sum, cumsum, prod and cumprod functions",
"topics": [
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]
},
{
"page": "Density",
"title": "Density Estimation with Telemetry",
"topics": [
"Density"
]
},
{
"page": "deriv_inverse.link",
"title": "Derivatives of inverse of link function (internal use)",
"topics": [
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"deriv_inverse.link"
]
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{
"page": "dipper",
"title": "Dipper capture-recapture data",
"topics": [
"dipper"
]
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{
"page": "Donovan.7",
"title": "Exercise 7 example data",
"topics": [
"Donovan.7"
]
},
{
"page": "Donovan.8",
"title": "Exercise 8 example data",
"topics": [
"Donovan.8"
]
},
{
"page": "edwards.eberhardt",
"title": "Rabbit capture-recapture data",
"topics": [
"edwards.eberhardt"
]
},
{
"page": "example.data",
"title": "Simulated data from Cormack-Jolly-Seber model",
"topics": [
"example.data"
]
},
{
"page": "export.chdata",
"title": "Export capture-history data to MARK .inp format",
"topics": [
"export.chdata"
]
},
{
"page": "export.MARK",
"title": "Export data and models for import in MARK",
"topics": [
"export.MARK"
]
},
{
"page": "export.model",
"title": "Export output files for appending into MARK .dbf/.fpt format",
"topics": [
"export.model"
]
},
{
"page": "extract.indices",
"title": "Various utility functions",
"topics": [
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"extract.indices",
"logitCI",
"nat.surv",
"pop.est",
"search.output.files"
]
},
{
"page": "extract.mark.output",
"title": "Extract results from MARK output file (internal use)",
"topics": [
"extract.mark.output"
]
},
{
"page": "fill.covariates",
"title": "Fill covariate entries in MARK design matrix with values",
"topics": [
"fill.covariates"
]
},
{
"page": "find.covariates",
"title": "Find covariates in MARK design matrix",
"topics": [
"find.covariates"
]
},
{
"page": "get.link",
"title": "Compute sets of link values for real parameters",
"topics": [
"get.link"
]
},
{
"page": "get.real",
"title": "Extract or compute sets of real parameters",
"topics": [
"get.real"
]
},
{
"page": "HidMarkov",
"title": "Hidden Markov Model",
"topics": [
"HidMarkov"
]
},
{
"page": "IELogitNormalMR",
"title": "Example of Immigration-Emigration LogitNormal Mark-Resight model",
"topics": [
"IELogitNormalMR"
]
},
{
"page": "import.chdata",
"title": "Import capture-recapture data sets from space or tab-delimited files",
"topics": [
"import.chdata"
]
},
{
"page": "inverse.link",
"title": "Inverse link functions (internal use)",
"topics": [
"inverse.link"
]
},
{
"page": "killdeer",
"title": "Killdeer nest survival example data",
"topics": [
"killdeer"
]
},
{
"page": "larksparrow",
"title": "Lark Sparrow",
"topics": [
"larksparrow",
"LASP"
]
},
{
"page": "load.model",
"title": "Load external model",
"topics": [
"load.model"
]
},
{
"page": "LogitNormalMR",
"title": "Example of LogitNormal Mark-Resight model",
"topics": [
"LogitNormalMR"
]
},
{
"page": "make.design.data",
"title": "Create design dataframes for MARK model specification",
"topics": [
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]
},
{
"page": "make.mark.model",
"title": "Create a MARK model for analysis",
"topics": [
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]
},
{
"page": "make.time.factor",
"title": "Make time-varying dummy variables from time-varying factor variable",
"topics": [
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]
},
{
"page": "mallard",
"title": "Mallard nest survival example",
"topics": [
"mallard"
]
},
{
"page": "mark",
"title": "Interface to MARK for fitting capture-recapture models",
"topics": [
"mark"
]
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{
"page": "mark.wrapper",
"title": "Constructs and runs a set of MARK models from a dataframe of parameter specifications",
"topics": [
"mark.wrapper"
]
},
{
"page": "mark.wrapper.parallel",
"title": "Constructs and runs in parallel a set of MARK models from a dataframe of parameter specifications",
"topics": [
"mark.wrapper.parallel"
]
},
{
"page": "mata.wald",
"title": "Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals",
"topics": [
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"tailarea.t",
"tailarea.z"
]
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{
"page": "merge_design.covariates",
"title": "Merge time (occasion) and/or group specific covariates into design data",
"topics": [
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"merge_design.covariates"
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"page": "merge.mark",
"title": "Merge mark model objects and lists of mark model objects",
"topics": [
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]
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{
"page": "model.average",
"title": "Compute model averaged estimates",
"topics": [
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"model.average.default"
]
},
{
"page": "model.average.list",
"title": "Compute model averaged estimates of real parameters from a list structure for estimates",
"topics": [
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]
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"page": "model.average.marklist",
"title": "Compute model averaged estimates of real parameters",
"topics": [
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]
},
{
"page": "model.table",
"title": "Create table of MARK model selection results",
"topics": [
"model.table"
]
},
{
"page": "MS_popan",
"title": "Convert Multistate data for POPAN-style abundance estimation",
"topics": [
"MS_popan"
]
},
{
"page": "MSJollySeber",
"title": "Multistate Jolly Seber",
"topics": [
"MSJollySeber"
]
},
{
"page": "mstrata",
"title": "Multistrata example data",
"topics": [
"mstrata"
]
},
{
"page": "MStruncate",
"title": "Truncate capture histories for multi-state models",
"topics": [
"MStruncate"
]
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{
"page": "NicholsMSOccupancy",
"title": "Multi-state occupancy example data",
"topics": [
"NicholsMSOccupancy"
]
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{
"page": "NSpeciesOcc",
"title": "Multiple Species Occupancy",
"topics": [
"NSpeciesOcc"
]
},
{
"page": "Paradise_shelduck",
"title": "Mulstistate Live-Dead Paradise Shelduck Data",
"topics": [
"Paradise_shelduck",
"ps"
]
},
{
"page": "PIMS",
"title": "Display PIM for a parameter",
"topics": [
"PIMS"
]
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{
"page": "Poisson_twoMR",
"title": "Example of Poisson Mark-Resight model",
"topics": [
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{
"page": "PoissonMR",
"title": "Example of Poisson Mark-Resight model",
"topics": [
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{
"page": "popan.derived",
"title": "Computes some derived abundance estimates for POPAN models",
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"popan.NGross",
"popan.Nt"
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{
"page": "predict_real",
"title": "Compute estimates of real parameters with individual and design covariates",
"topics": [
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]
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{
"page": "print.mark",
"title": "Print MARK objects",
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"print.mark"
]
},
{
"page": "print.marklist",
"title": "Print MARK list objects",
"topics": [
"print.marklist"
]
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{
"page": "print.summary.mark",
"title": "Prints summary of MARK model parameters and results",
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]
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{
"page": "process.ch",
"title": "Process release-recapture history data",
"topics": [
"process.ch"
]
},
{
"page": "process.data",
"title": "Process encounter history dataframe for MARK analysis",
"topics": [
"process.data"
]
},
{
"page": "RDMultScalOcc",
"title": "Multi-scale dynamic occupancy models in RMark",
"topics": [
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]
},
{
"page": "RDOccupancy",
"title": "Robust Design occupancy example data",
"topics": [
"RDOccupancy"
]
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{
"page": "RDSalamander",
"title": "Robust design salamander occupancy data",
"topics": [
"RDSalamander"
]
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{
"page": "readMarkVcv",
"title": "Reads binary file output from MARK and returns a list of the results",
"topics": [
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"readMarkVcv"
]
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{
"page": "release.gof",
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"topics": [
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]
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{
"page": "remove.mark",
"title": "Remove mark models from list",
"topics": [
"remove.mark"
]
},
{
"page": "rerun.mark",
"title": "Runs a previous MARK model with new starting values",
"topics": [
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]
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{
"page": "robust",
"title": "Robust design example data",
"topics": [
"robust"
]
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{
"page": "run.mark.model",
"title": "Runs analysis with MARK model using MARK.EXE",
"topics": [
"run.mark.model"
]
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{
"page": "run.models",
"title": "Runs a set of MARK models",
"topics": [
"run.models"
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{
"page": "salamander",
"title": "Salamander occupancy data",
"topics": [
"salamander"
]
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{
"page": "setup.model",
"title": "Defines model specific parameters (internal use)",
"topics": [
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"title": "Setup parameter structure specific to model (internal use)",
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{
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"title": "An example of the Multistrata (multi-state) model in which states are routes taken by migrating fish.",
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]
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{
"page": "splitCH",
"title": "Split/collapse capture histories",
"topics": [
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"splitCH"
]
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{
"page": "store",
"title": "Store models externally or restore to workspace from external storage",
"topics": [
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"store"
]
},
{
"page": "strip.comments",
"title": "Strip comments",
"topics": [
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{
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"title": "Provides a summary for the capture histories",
"topics": [
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"summary_ch"
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{
"page": "summary.mark",
"title": "Summary of MARK model parameters and results",
"topics": [
"summary.mark"
]
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{
"page": "TransitionMatrix",
"title": "Multi-state Transition Functions",
"topics": [
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"transition.pairs",
"TransitionMatrix"
]
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{
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"title": "Determine validity of parameters for a model (internal use)",
"topics": [
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"title": "Variance components estimation",
"topics": [
"var.components"
]
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{
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"title": "Variance components estimation using REML or maximum likelihood",
"topics": [
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{
"page": "weta",
"title": "Occupancy data for Mahoenui Giant Weta",
"topics": [
"weta"
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{
"page": "Whatsnew",
"title": "Summary of changes by version",
"topics": [
"Whatsnew"
]
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{
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"title": "White-winged dove Jolly-Seber POPAN Analysis Details",
"topics": [
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"wwdo.10",
"wwdo.popan"
]
}
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