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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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Version

Install

install.packages('RMark')

Monthly Downloads

1,692

Version

3.0.0

License

GPL (>= 2)

Maintainer

Last Published

August 13th, 2022

Functions in RMark (3.0.0)

Exercise 8 example data

Multiple Species Occupancy

Example of Poisson Mark-Resight model

Example of Poisson Mark-Resight model

Robust design salamander occupancy data

Density Estimation with Telemetry

Burnham Live-Dead Model

Multi-scale dynamic occupancy models in RMark

NicholsMSOccupancy

Multi-state occupancy example data

TransitionMatrix

Multi-state Transition Functions

Robust Design occupancy example data

Collect MARK models into a list and optionally construct a table of model results

MARK model beta parameters

Removes unused MARK output files

collect.model.names

Collect names of MARK model objects from list of R objects (internal function)

San Luis Valley mallard data

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 estimates of link values

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 estimates of real parameters

Simulated data from Cormack-Jolly-Seber model

Export data and models for import in MARK

covariate.predictions

Compute estimates of real parameters for multiple covariate values

Load external model

Killdeer nest survival example data

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

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 functions (internal use)

Import capture-recapture data sets from space or tab-delimited files

create.model.list

Creates a dataframe of all combinations of parameter specifications

Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals

fill.covariates

Fill covariate entries in MARK design matrix with values

White-tailed deer double observer spotlight capture-recapture analysis

add.design.data

Add design data

Runs analysis with MARK model using MARK.EXE

find.covariates

Find covariates in MARK design matrix

Summary of changes by version

Runs a set of MARK models

merge_design.covariates

Merge time (occasion) and/or group specific covariates into design data

Dipper capture-recapture data

edwards.eberhardt

Rabbit capture-recapture data

Interface to MARK for fitting capture-recapture models

Mallard nest survival example

Constructs and runs a set of MARK models from a dataframe of parameter specifications

Process encounter history dataframe for MARK analysis

Create table of MARK model selection results

Compute model averaged estimates

Multistrata example data

Merge mark model objects and lists of mark model objects

Summary of MARK model parameters and results

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

Compute estimates of real parameters with individual and design covariates

Runs a previous MARK model with new starting values

Reads binary file output from MARK and returns a list of the results

Computes some derived abundance estimates for POPAN models

create.mark.mcmc

Create mcmc object for analysis with coda

Process release-recapture history data

Example data for Closed Robust Design Multistrata

print.summary.mark

Prints summary of MARK model parameters and results

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

Variance components estimation

var.components.reml

Variance components estimation using REML or maximum likelihood

Remove mark models from list

Defines model specific parameters (internal use)

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)

Compute sets of link values for real parameters

Robust design example data

Export output files for appending into MARK .dbf/.fpt format

Export capture-history data to MARK .inp format

Extract or compute sets of real parameters

valid.parameters

Determine validity of parameters for a model (internal use)

Provides a summary for the capture histories

make.mark.model

Create a MARK model for analysis

Occupancy data for Mahoenui Giant Weta

White-winged dove Jolly-Seber POPAN Analysis Details

Print MARK list objects

Split/collapse capture histories

Store models externally or restore to workspace from external storage

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

Black duck known fate data

Example of LogitNormal Mark-Resight model

Exercise 7 example data

Convert Multistate data for POPAN-style abundance estimation

Truncate capture histories for multi-state models