RMark: R Code for Mark Analysis

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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.

Author
Jeff 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 publication
2016-12-02 10:49:14
Maintainer
Jeff Laake <jefflaake@gmail.com>
License
GPL (>= 2)
Version
2.2.2

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

Files in this package

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