Package: RMark 3.0.0

RMark: R Code for Mark Analysis

An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at <http://www.phidot.org/software/mark/downloads/> but is not open source.

Authors:Jeff Laake <[email protected]> with code contributions from Eldar Rakhimberdiev, Ben Augustine, Daniel Turek, Brett McClintock, and Jim Hines and example data and analysis from Bret Collier, Jay Rotella, David Pavlacky, Andrew Paul, Luke Eberhart- Phillips, Jake Ivan, and Connor Wood.

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RMark.pdf |RMark.html✨
RMark/json (API)
NEWS

# Install 'RMark' in R:
install.packages('RMark', repos = c('https://jlaake.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • Blackduck - Black duck known fate data
  • Density - Density Estimation with Telemetry
  • Donovan.7 - Exercise 7 example data
  • Donovan.8 - Exercise 8 example data
  • IELogitNormalMR - Example of Immigration-Emigration LogitNormal Mark-Resight model
  • LASP - Lark Sparrow
  • LogitNormalMR - Example of LogitNormal Mark-Resight model
  • NSpeciesOcc - Multiple Species Occupancy
  • NicholsMSOccupancy - Multi-state occupancy example data
  • PoissonMR - Example of Poisson Mark-Resight model
  • Poisson_twoMR - Example of Poisson Mark-Resight model
  • RDOccupancy - Robust Design occupancy example data
  • RDSalamander - Robust design salamander occupancy data
  • brownie - San Luis Valley mallard data
  • crdms - Example data for Closed Robust Design Multistrata
  • deer - White-tailed deer double observer spotlight capture-recapture analysis
  • dipper - Dipper capture-recapture data
  • edwards.eberhardt - Rabbit capture-recapture data
  • example.data - Simulated data from Cormack-Jolly-Seber model
  • killdeer - Killdeer nest survival example data
  • mallard - Mallard nest survival example
  • mstrata - Multistrata example data
  • ps - Mulstistate Live-Dead Paradise Shelduck Data
  • robust - Robust design example data
  • salamander - Salamander occupancy data
  • weta - Occupancy data for Mahoenui Giant Weta
  • wwdo.09 - White-winged dove Jolly-Seber POPAN Analysis Details
  • wwdo.10 - White-winged dove Jolly-Seber POPAN Analysis Details

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.77 score 4 packages 366 scripts 1.3k downloads 96 mentions 66 exports 20 dependencies

Last updated 3 years agofrom:b65cae31b0. Checks:1 OK, 8 ERROR. Indexed: yes.

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Exports:add.design.dataadjust.chatadjust.parameter.countadjust.valuecleanupcoef.markcollapseCHcollect.model.namescollect.modelscompute.realcompute.Snconvert.inpcovariate.predictionscreate.mark.mcmccreate.model.listdeltamethod.specialexport.chdataexport.MARKexport.modelextract.indicesfill.covariatesfind.covariatesfind.possible.transitionsget.realimport.chdatalogitCImake.design.datamake.mark.modelmake.time.factormarkmark.wrappermark.wrapper.parallelmata.waldmerge_design.covariatesmerge.markmodel.averagemodel.tableMS_popanMStruncatenat.survPIMSpop.estpopan.derivedpredict_realprint.marklistprint.summary.markprocess.chprocess.datareadMarkVcvrelease.gofremove.markrerun.markrestorerun.mark.modelrun.modelssearch.output.filessetup.modelsetup.parameterssplitCHstoresummary_chsummary.marktransition.pairsTransitionMatrixvar.componentsvar.components.reml

Dependencies:clicodaexpmfansigenericsgluelatticelifecyclemagrittrMatrixmatrixcalcmsmmvtnormpillarpkgconfigrlangsurvivaltibbleutf8vctrs

Readme and manuals

Help Manual

Help pageTopics
A beginners introduction and guide to RMarkABeginnersGuide
Add design dataadd.design.data
Adjust count of estimated parametersadjust.parameter.count
Adjust over-dispersion scale or a result value such as effective sample sizeadjust.chat adjust.value
Black duck known fate dataBlackduck
San Luis Valley mallard databrownie
Burnham Live-Dead ModelBurnham
Removes unused MARK output filescleanup
MARK model beta parameterscoef.mark
Collect names of MARK model objects from list of R objects (internal function)collect.model.names
Collect MARK models into a list and optionally construct a table of model resultscollect.models
Compute design data for a specific parameter in the MARK model (internal use)compute.design.data
Compute estimates of link valuescompute.link
Compute link values from real parameterscompute.links.from.reals
Compute estimates of real parameterscompute.real
Convert MARK input file to RMark dataframeconvert.inp
Convert link values to real parametersconvert.link.to.real
Compute estimates of real parameters for multiple covariate valuescovariate.predictions
Example data for Closed Robust Design Multistratacrdms
Create mcmc object for analysis with codacreate.mark.mcmc
Creates a dataframe of all combinations of parameter specificationscreate.model.list
White-tailed deer double observer spotlight capture-recapture analysisdeer
Compute delta method variance for sum, cumsum, prod and cumprod functionsdeltamethod.special
Density Estimation with TelemetryDensity
Derivatives of inverse of link function (internal use)deriv.inverse.link deriv_inverse.link
Dipper capture-recapture datadipper
Exercise 7 example dataDonovan.7
Exercise 8 example dataDonovan.8
Rabbit capture-recapture dataedwards.eberhardt
Simulated data from Cormack-Jolly-Seber modelexample.data
Export capture-history data to MARK .inp formatexport.chdata
Export data and models for import in MARKexport.MARK
Export output files for appending into MARK .dbf/.fpt formatexport.model
Various utility functionscompute.Sn extract.indices logitCI nat.surv pop.est search.output.files
Extract results from MARK output file (internal use)extract.mark.output
Fill covariate entries in MARK design matrix with valuesfill.covariates
Find covariates in MARK design matrixfind.covariates
Compute sets of link values for real parametersget.link
Extract or compute sets of real parametersget.real
Example of Immigration-Emigration LogitNormal Mark-Resight modelIELogitNormalMR
Import capture-recapture data sets from space or tab-delimited filesimport.chdata
Inverse link functions (internal use)inverse.link
Killdeer nest survival example datakilldeer
Lark Sparrowlarksparrow LASP
Load external modelload.model
Example of LogitNormal Mark-Resight modelLogitNormalMR
Create design dataframes for MARK model specificationmake.design.data
Create a MARK model for analysismake.mark.model
Make time-varying dummy variables from time-varying factor variablemake.time.factor
Mallard nest survival examplemallard
Interface to MARK for fitting capture-recapture modelsmark
Constructs and runs a set of MARK models from a dataframe of parameter specificationsmark.wrapper
Constructs and runs in parallel a set of MARK models from a dataframe of parameter specificationsmark.wrapper.parallel
Model-Averaged Tail Area Wald (MATA-Wald) confidence intervalsmata.wald tailarea.t tailarea.z
Merge time (occasion) and/or group specific covariates into design datamerge.design.covariates merge_design.covariates
Merge mark model objects and lists of mark model objectsmerge.mark
Compute model averaged estimatesmodel.average model.average.default
Compute model averaged estimates of real parameters from a list structure for estimatesmodel.average.list
Compute model averaged estimates of real parametersmodel.average.marklist
Create table of MARK model selection resultsmodel.table
Convert Multistate data for POPAN-style abundance estimationMS_popan
Multistrata example datamstrata
Truncate capture histories for multi-state modelsMStruncate
Multi-state occupancy example dataNicholsMSOccupancy
Multiple Species OccupancyNSpeciesOcc
Mulstistate Live-Dead Paradise Shelduck DataParadise_shelduck ps
Display PIM for a parameterPIMS
Example of Poisson Mark-Resight modelPoisson_twoMR
Example of Poisson Mark-Resight modelPoissonMR
Computes some derived abundance estimates for POPAN modelspopan.derived popan.NGross popan.Nt
Compute estimates of real parameters with individual and design covariatespredict_real
Print MARK objectsprint.mark
Print MARK list objectsprint.marklist
Prints summary of MARK model parameters and resultsprint.summary.mark
Process release-recapture history dataprocess.ch
Process encounter history dataframe for MARK analysisprocess.data
Multi-scale dynamic occupancy models in RMarkRDMultScalOcc
Robust Design occupancy example dataRDOccupancy
Robust design salamander occupancy dataRDSalamander
Reads binary file output from MARK and returns a list of the resultsread.mark.binary readMarkVcv
Runs RELEASE for goodness of fit testrelease.gof
Remove mark models from listremove.mark
Runs a previous MARK model with new starting valuesrerun.mark
Robust design example datarobust
Runs analysis with MARK model using MARK.EXErun.mark.model
Runs a set of MARK modelsrun.models
Salamander occupancy datasalamander
Defines model specific parameters (internal use)setup.model
Setup parameter structure specific to model (internal use)setup.parameters
An example of the Multistrata (multi-state) model in which states are routes taken by migrating fish.skagit
Split/collapse capture historiescollapseCH splitCH
Store models externally or restore to workspace from external storagerestore store
Strip commentsstrip.comments
Provides a summary for the capture historiessummary.ch summary_ch
Summary of MARK model parameters and resultssummary.mark
Multi-state Transition Functionsfind.possible.transitions transition.pairs TransitionMatrix
Determine validity of parameters for a model (internal use)valid.parameters
Variance components estimationvar.components
Variance components estimation using REML or maximum likelihoodvar.components.reml
Occupancy data for Mahoenui Giant Wetaweta
Summary of changes by versionWhatsnew
White-winged dove Jolly-Seber POPAN Analysis Detailswwdo.09 wwdo.10 wwdo.popan