RMark: R Code for Mark Analysis
Version 2.2.2

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 but is not open source.

AuthorJeff Laake <jeff.laake@noaa.gov> with code contributions from Eldar Rakhimberdiev, Ben Augustine and Daniel Turek, and example data and analysis from Bret Collier, Jay Rotella, David Pavlacky,Andrew Paul and Luke Eberhart- Phillips.
Date of publication2016-12-02 10:49:14
MaintainerJeff Laake <jefflaake@gmail.com>
LicenseGPL (>= 2)
Version2.2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RMark")

Popular man pages

ABeginnersGuide: A beginners introduction and guide to RMark
deer: White-tailed deer double observer spotlight capture-recapture...
deltamethod.special: Compute delta method variance for sum, cumsum, prod and...
dipper: Dipper capture-recapture data
export.chdata: Export capture-history data to MARK .inp format
mallard: Mallard nest survival example
predict_real: Compute estimates of real parameters with individual and...
See all...

All man pages Function index File listing

Man pages

ABeginnersGuide: A beginners introduction and guide to RMark
add.design.data: Add design data
adjust.parameter.count: Adjust count of estimated parameters
adjust.value: Adjust over-dispersion scale or a result value such as...
Blackduck: Black duck known fate data
brownie: San Luis Valley mallard data
Burnham: #' Burnham Live-Dead Model
cleanup: Removes unused MARK output files
coef.mark: MARK model beta parameters
collect.model.names: Collect names of MARK model objects from list of R objects...
collect.models: Collect MARK models into a list and optionally construct a...
compute.design.data: Compute design data for a specific parameter in the MARK...
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...
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...
deer: White-tailed deer double observer spotlight capture-recapture...
deltamethod.special: Compute delta method variance for sum, cumsum, prod and...
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
IELogitNormalMR: Example of Immigration-Emigration LogitNormal Mark-Resight...
import.chdata: Import capture-recapture data sets from space or...
inverse.link: Inverse link functions (internal use)
killdeer: Killdeer nest survival example data
larksparrow: Lark Sparrow
load.model: Load external model
LogitNormalMR: Example of LogitNormal Mark-Resight model
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...
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...
mark.wrapper.parallel: Constructs and runs in parallel a set of MARK models from a...
mata.wald: Model-Averaged Tail Area Wald (MATA-Wald) confidence...
merge_design.covariates: Merge time (occasion) and/or group specific covariates into...
merge.mark: Merge mark model objects and lists of mark model objects
model.average: Compute model averaged estimates
model.average.list: Compute model averaged estimates of real parameters from a...
model.average.marklist: Compute model averaged estimates of real parameters
model.table: Create table of MARK model selection results
MS_popan: Convert Multistate data for POPAN-style abundance estimation
mstrata: Multistrata example data
MStruncate: Truncate capture histories for multi-state models
NicholsMSOccupancy: Multi-state occupancy example data
PIMS: Display PIM for a parameter
PoissonMR: Example of Poisson Mark-Resight model
Poisson_twoMR: Example of Poisson Mark-Resight model
popan.derived: Computes some derived abundance estimates for POPAN models
predict_real: Compute estimates of real parameters with individual and...
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
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...
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
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)
skagit: An example of the Mulstistrata (multi-state) model in which...
splitCH: Split/collapse capture histories
store: Store models externally or restore to workspace from external...
strip.comments: Strip comments
summary_ch: Provides a summary for the capture histories
summary.mark: Summary of MARK model parameters and results
TransitionMatrix: Multi-state Transition Functions
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...
weta: Occupancy data for Mahoenui Giant Weta
Whatsnew: Summary of changes by version
wwdo.popan: White-winged dove Jolly-Seber POPAN Analysis Details

Functions

ABeginnersGuide Man page
Blackduck Man page
Burnham Man page
Donovan.7 Man page
Donovan.8 Man page
IELogitNormalMR Man page
LASP Man page
LogitNormalMR Man page
MS_popan Man page Source code
MStruncate Man page Source code
NicholsMSOccupancy Man page
PIMS Man page Source code
PoissonMR Man page
Poisson_twoMR Man page
RDOccupancy Man page
RDSalamander Man page
TransitionMatrix Man page Source code
Whatsnew Man page
add.design.data Man page Source code
adjust.chat Man page Source code
adjust.parameter.count Man page Source code
adjust.value Man page Source code
brownie Man page
checkForMark Source code
cleanup Man page Source code
coef.mark Man page Source code
collapseCH Man page Source code
collect.model.names Man page Source code
collect.models Man page Source code
compute.Sn Man page Source code
compute.design.data Man page Source code
compute.link Man page Source code
compute.links.from.reals Man page Source code
compute.real Man page Source code
convert.inp Man page Source code
convert.link.to.real Man page Source code
covariate.predictions Man page Source code
crdms Man page
create.mark.mcmc Man page Source code
create.model.list Man page Source code
create_markpath Source code
deer Man page
deltamethod.special Man page Source code
deriv.inverse.link Man page
deriv_inverse.link Man page Source code
dipper Man page
edwards.eberhardt Man page
example.data Man page
export.MARK Man page Source code
export.chdata Man page Source code
export.model Man page Source code
extract.indices Man page Source code
extract.mark.output Man page Source code
fill.covariates Man page Source code
find.covariates Man page Source code
find.possible.transitions Man page Source code
get.link Man page Source code
get.real Man page Source code
import.chdata Man page Source code
inverse.link Man page Source code
killdeer Man page
larksparrow Man page
load.model Man page Source code
logitCI Man page Source code
make.design.data Man page Source code
make.mark.model Man page Source code
make.run.mark.model.apply.int Source code
make.time.factor Man page Source code
mallard Man page
mark Man page Source code
mark.wrapper Man page Source code
mark.wrapper.parallel Man page Source code
mata.wald Man page Source code
merge.design.covariates Man page
merge.mark Man page Source code
merge_design.covariates Man page Source code
model.average Man page Source code
model.average.default Man page Source code
model.average.list Man page Source code
model.average.marklist Man page Source code
model.table Man page Source code
mstrata Man page
nat.surv Man page Source code
onAttach Source code
pop.est Man page Source code
popan.NGross Man page Source code
popan.Nt Man page Source code
popan.derived Man page Source code
predict_real Man page Source code
print.RMark.version Source code
print.mark Man page Source code
print.marklist Man page Source code
print.summary.mark Man page Source code
process.ch Man page Source code
process.data Man page Source code
read.mark.binary Man page Source code
read.mark.binary.linux Man page Source code
release.gof Man page Source code
remove.mark Man page Source code
rerun.mark Man page Source code
restore Man page Source code
robust Man page
run.mark.model Man page Source code
run.models Man page Source code
salamander Man page
search.output.files Man page Source code
setup.model Man page Source code
setup.parameters Man page Source code
skagit Man page
splitCH Man page Source code
store Man page Source code
strip.comments Man page Source code
summary.ch Man page
summary.mark Man page Source code
summary_ch Man page Source code
tailarea.t Man page Source code
tailarea.z Man page Source code
transition.pairs Man page Source code
valid.parameters Man page Source code
var.components Man page Source code
var.components.reml Man page Source code
weta Man page
wwdo.09 Man page
wwdo.10 Man page
wwdo.popan Man page

Files

inst
inst/MarkModels.pdf
inst/parameters.txt
inst/CITATION
inst/models.txt
inst/DerivedPar.txt
inst/README.txt
inst/extdata
inst/extdata/young.inp
inst/extdata/effect_size.inp
inst/extdata/brownie.inp
inst/extdata/mstrata.txt
inst/extdata/huggins.inp
inst/extdata/ms_cjs.inp
inst/extdata/cjs3grp.inp
inst/extdata/ed_males.inp
inst/extdata/dipper.inp
inst/extdata/linear.inp
inst/extdata/rd_complex1.inp
inst/extdata/salamander.inp
inst/extdata/simple_closed1.inp
inst/extdata/ms_rdsimple1.inp
inst/extdata/adult.inp
inst/extdata/blckduck.inp
inst/extdata/island.inp
inst/extdata/age-transients-full.inp
inst/extdata/chase.inp
inst/extdata/mallardnestexample.inp
inst/extdata/f_age.inp
inst/extdata/age_ya.inp
inst/extdata/capsid.inp
inst/extdata/indcov2.inp
inst/extdata/robust.inp
inst/extdata/robust.txt
inst/extdata/example.data.txt
inst/extdata/age.inp
inst/extdata/mixed_closed1.inp
inst/extdata/recruit-ms.inp
inst/extdata/ed.inp
inst/extdata/multi_group.inp
inst/extdata/mssurv.inp
inst/extdata/ld1.inp
inst/extdata/weta.txt
inst/extdata/killdeer.inp
inst/extdata/ms_directional.inp
inst/extdata/pass3mstrata5.inp
inst/extdata/plover_mark.inp
inst/extdata/nicholsmsoccupancy.inp
inst/extdata/mallard.txt
inst/extdata/transient.inp
inst/extdata/deer.inp
inst/extdata/effect_size3.inp
inst/extdata/m_age.inp
inst/extdata/rd_simple1.inp
inst/extdata/donovan.8.inp
inst/extdata/aa.inp
inst/extdata/killdeer.txt
inst/extdata/edwardsandeberhardt.inp
inst/extdata/ms_gof.inp
inst/extdata/indcov1.inp
inst/extdata/donovan.7.inp
inst/extdata/brownadt.inp
inst/extdata/clogit_demo.inp
inst/extdata/rdsalamander.inp
inst/extdata/interval.inp
inst/extdata/dipper.txt
inst/extdata/edwardsandeberhardt.txt
inst/extdata/staggered.inp
inst/extdata/skagit.txt
inst/extdata/yngadt.inp
inst/extdata/blackduck.txt
NAMESPACE
NEWS
data
data/example.data.rda
data/salamander.rda
data/mallard.rda
data/LASP.rda
data/mstrata.rda
data/dipper.rda
data/Poisson_twoMR.rda
data/robust.rda
data/RDOccupancy.rda
data/crdms.rda
data/Blackduck.rda
data/PoissonMR.rda
data/Donovan.7.rda
data/edwards.eberhardt.rda
data/Donovan.8.rda
data/NicholsMSOccupancy.rda
data/deer.rda
data/wwdo.10.rda
data/killdeer.rda
data/RDSalamander.rda
data/IELogitNormalMR.rda
data/wwdo.09.rda
data/weta.rda
data/brownie.rda
data/LogitNormalMR.rda
R
R/release.gof.R
R/get.link.R
R/TransitionMatrix.R
R/var.components.R
R/mark.R
R/compute.real.R
R/cleanup.R
R/create.mark.mcmc.R
R/setup.parameters.R
R/popan.r
R/run.mark.model.R
R/convert.link.to.real.r
R/covariate.predictions.r
R/model.average.list.r
R/run.models.R
R/export.MARK.r
R/store.r
R/mark.wrapper.parallel.r
R/process.data.R
R/summary.mark.R
R/read.mark.binary.linux.R
R/create.model.list.R
R/setup.model.R
R/model.average.R
R/rerun.mark.R
R/collect.models.R
R/export.model.r
R/fill.covariates.R
R/valid.parameters.R
R/extract.mark.output.R
R/splitCH.r
R/add.design.data.R
R/inverse.link.R
R/read.mark.binary.R
R/print.summary.mark.R
R/adjust.chat.R
R/make.design.data.R
R/predict_real.R
R/model.average.marklist.R
R/import.chdata.R
R/convert.inp.r
R/var.components.reml.r
R/mark.wrapper.R
R/adjust.parameter.count.R
R/get.real.R
R/compute.links.from.reals.R
R/PIMS.R
R/find.covariates.R
R/compute.design.data.R
R/model.average.default.r
R/mata.wald.r
R/model.table.R
R/remove.mark.r
R/collect.model.names.R
R/utility.r
R/compute.link.R
R/deltamethod.r
R/summary.ch.r
R/deriv.inverse.link.R
R/process.ch.R
R/merge.design.covariates.r
R/make.time.factor.r
R/make.mark.model.R
R/merge.mark.r
R/export.chdata.R
R/print.mark.R
R/zzz.R
R/RMark-package.R
MD5
DESCRIPTION
man
man/merge_design.covariates.Rd
man/larksparrow.Rd
man/valid.parameters.Rd
man/Burnham.Rd
man/LogitNormalMR.Rd
man/process.data.Rd
man/NicholsMSOccupancy.Rd
man/Poisson_twoMR.Rd
man/get.link.Rd
man/MS_popan.Rd
man/process.ch.Rd
man/find.covariates.Rd
man/collect.model.names.Rd
man/mstrata.Rd
man/mata.wald.Rd
man/weta.Rd
man/edwards.eberhardt.Rd
man/export.MARK.Rd
man/compute.links.from.reals.Rd
man/create.model.list.Rd
man/print.mark.Rd
man/cleanup.Rd
man/convert.inp.Rd
man/MStruncate.Rd
man/mark.Rd
man/make.time.factor.Rd
man/PoissonMR.Rd
man/run.models.Rd
man/model.average.marklist.Rd
man/strip.comments.Rd
man/wwdo.popan.Rd
man/setup.model.Rd
man/example.data.Rd
man/summary_ch.Rd
man/inverse.link.Rd
man/run.mark.model.Rd
man/summary.mark.Rd
man/store.Rd
man/deer.Rd
man/IELogitNormalMR.Rd
man/export.model.Rd
man/mallard.Rd
man/deriv_inverse.link.Rd
man/robust.Rd
man/add.design.data.Rd
man/deltamethod.special.Rd
man/create.mark.mcmc.Rd
man/extract.mark.output.Rd
man/adjust.value.Rd
man/export.chdata.Rd
man/mark.wrapper.Rd
man/release.gof.Rd
man/compute.real.Rd
man/killdeer.Rd
man/var.components.reml.Rd
man/skagit.Rd
man/make.design.data.Rd
man/Blackduck.Rd
man/convert.link.to.real.Rd
man/adjust.parameter.count.Rd
man/setup.parameters.Rd
man/Donovan.8.Rd
man/read.mark.binary.Rd
man/coef.mark.Rd
man/compute.link.Rd
man/model.table.Rd
man/make.mark.model.Rd
man/rerun.mark.Rd
man/crdms.Rd
man/var.components.Rd
man/predict_real.Rd
man/model.average.list.Rd
man/TransitionMatrix.Rd
man/mark.wrapper.parallel.Rd
man/print.summary.mark.Rd
man/fill.covariates.Rd
man/import.chdata.Rd
man/RDSalamander.Rd
man/collect.models.Rd
man/splitCH.Rd
man/covariate.predictions.Rd
man/RDOccupancy.Rd
man/popan.derived.Rd
man/get.real.Rd
man/extract.indices.Rd
man/PIMS.Rd
man/model.average.Rd
man/ABeginnersGuide.Rd
man/Donovan.7.Rd
man/remove.mark.Rd
man/load.model.Rd
man/brownie.Rd
man/Whatsnew.Rd
man/dipper.Rd
man/print.marklist.Rd
man/salamander.Rd
man/merge.mark.Rd
man/compute.design.data.Rd
RMark documentation built on May 19, 2017, 11:24 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.