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.

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

View on CRAN

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

Files

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

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