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RMark (version 3.0.0)
R Code for Mark Analysis
Description
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.
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3.0.0
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Install
install.packages('RMark')
Monthly Downloads
1,447
Version
3.0.0
License
GPL (>= 2)
Maintainer
Jeff Laake
Last Published
August 13th, 2022
Functions in RMark (3.0.0)
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Donovan.8
Exercise 8 example data
NSpeciesOcc
Multiple Species Occupancy
PoissonMR
Example of Poisson Mark-Resight model
Poisson_twoMR
Example of Poisson Mark-Resight model
RDSalamander
Robust design salamander occupancy data
Density
Density Estimation with Telemetry
Burnham
Burnham Live-Dead Model
RDMultScalOcc
Multi-scale dynamic occupancy models in RMark
NicholsMSOccupancy
Multi-state occupancy example data
TransitionMatrix
Multi-state Transition Functions
RDOccupancy
Robust Design occupancy example data
collect.models
Collect MARK models into a list and optionally construct a table of model results
coef.mark
MARK model beta parameters
cleanup
Removes unused MARK output files
collect.model.names
Collect names of MARK model objects from list of R objects (internal function)
brownie
San Luis Valley mallard data
adjust.value
Adjust over-dispersion scale or a result value such as effective sample size
adjust.parameter.count
Adjust count of estimated parameters
compute.links.from.reals
Compute link values from real parameters
compute.link
Compute estimates of link values
PIMS
Display PIM for a parameter
compute.design.data
Compute design data for a specific parameter in the MARK model (internal use)
convert.link.to.real
Convert link values to real parameters
compute.real
Compute estimates of real parameters
example.data
Simulated data from Cormack-Jolly-Seber model
export.MARK
Export data and models for import in MARK
covariate.predictions
Compute estimates of real parameters for multiple covariate values
load.model
Load external model
killdeer
Killdeer nest survival example data
convert.inp
Convert MARK input file to RMark dataframe
deltamethod.special
Compute delta method variance for sum, cumsum, prod and cumprod functions
make.design.data
Create design dataframes for MARK model specification
larksparrow
Lark Sparrow
Paradise_shelduck
Mulstistate Live-Dead Paradise Shelduck Data
extract.indices
Various utility functions
deriv_inverse.link
Derivatives of inverse of link function (internal use)
extract.mark.output
Extract results from MARK output file (internal use)
inverse.link
Inverse link functions (internal use)
import.chdata
Import capture-recapture data sets from space or tab-delimited files
create.model.list
Creates a dataframe of all combinations of parameter specifications
mata.wald
Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
fill.covariates
Fill covariate entries in MARK design matrix with values
deer
White-tailed deer double observer spotlight capture-recapture analysis
add.design.data
Add design data
run.mark.model
Runs analysis with MARK model using MARK.EXE
find.covariates
Find covariates in MARK design matrix
Whatsnew
Summary of changes by version
run.models
Runs a set of MARK models
merge_design.covariates
Merge time (occasion) and/or group specific covariates into design data
dipper
Dipper capture-recapture data
edwards.eberhardt
Rabbit capture-recapture data
mark
Interface to MARK for fitting capture-recapture models
mallard
Mallard nest survival example
mark.wrapper
Constructs and runs a set of MARK models from a dataframe of parameter specifications
process.data
Process encounter history dataframe for MARK analysis
model.table
Create table of MARK model selection results
model.average
Compute model averaged estimates
mstrata
Multistrata example data
merge.mark
Merge mark model objects and lists of mark model objects
strip.comments
Strip comments
summary.mark
Summary of MARK model parameters and results
salamander
Salamander occupancy data
model.average.list
Compute model averaged estimates of real parameters from a list structure for estimates
model.average.marklist
Compute model averaged estimates of real parameters
predict_real
Compute estimates of real parameters with individual and design covariates
rerun.mark
Runs a previous MARK model with new starting values
readMarkVcv
Reads binary file output from MARK and returns a list of the results
popan.derived
Computes some derived abundance estimates for POPAN models
create.mark.mcmc
Create mcmc object for analysis with coda
process.ch
Process release-recapture history data
crdms
Example data for Closed Robust Design Multistrata
print.summary.mark
Prints summary of MARK model parameters and results
release.gof
Runs RELEASE for goodness of fit test
mark.wrapper.parallel
Constructs and runs in parallel a set of MARK models from a dataframe of parameter specifications
var.components
Variance components estimation
var.components.reml
Variance components estimation using REML or maximum likelihood
remove.mark
Remove mark models from list
setup.model
Defines model specific parameters (internal use)
skagit
An example of the Multistrata (multi-state) model in which states are routes taken by migrating fish.
setup.parameters
Setup parameter structure specific to model (internal use)
get.link
Compute sets of link values for real parameters
robust
Robust design example data
export.model
Export output files for appending into MARK .dbf/.fpt format
export.chdata
Export capture-history data to MARK .inp format
get.real
Extract or compute sets of real parameters
valid.parameters
Determine validity of parameters for a model (internal use)
summary_ch
Provides a summary for the capture histories
make.mark.model
Create a MARK model for analysis
weta
Occupancy data for Mahoenui Giant Weta
wwdo.popan
White-winged dove Jolly-Seber POPAN Analysis Details
print.marklist
Print MARK list objects
splitCH
Split/collapse capture histories
store
Store models externally or restore to workspace from external storage
print.mark
Print MARK objects
make.time.factor
Make time-varying dummy variables from time-varying factor variable
IELogitNormalMR
Example of Immigration-Emigration LogitNormal Mark-Resight model
ABeginnersGuide
A beginners introduction and guide to RMark
Blackduck
Black duck known fate data
LogitNormalMR
Example of LogitNormal Mark-Resight model
Donovan.7
Exercise 7 example data
MS_popan
Convert Multistate data for POPAN-style abundance estimation
MStruncate
Truncate capture histories for multi-state models