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RMark (version 2.2.7)

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

23,521

Version

2.2.7

License

GPL (>= 2)

Maintainer

Jeff Laake

Last Published

November 6th, 2019

Functions in RMark (2.2.7)

Black duck known fate data

IELogitNormalMR

Example of Immigration-Emigration LogitNormal Mark-Resight model

Density Estimation with Telemetry

ABeginnersGuide

A beginners introduction and guide to RMark

Exercise 8 example data

Example of LogitNormal Mark-Resight model

Burnham Live-Dead Model

Exercise 7 example data

Truncate capture histories for multi-state models

Convert Multistate data for POPAN-style abundance estimation

Display PIM for a parameter

NicholsMSOccupancy

Multi-state occupancy example data

Multiple Species Occupancy

Paradise_shelduck

Mulstistate Live-Dead Paradise Shelduck Data

TransitionMatrix

Multi-state Transition Functions

Robust design salamander occupancy data

Example of Poisson Mark-Resight model

Example of Poisson Mark-Resight model

Multi-scale dynamic occupancy models in RMark

Robust Design occupancy example data

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

compute.design.data

Compute design data for a specific parameter in the MARK model (internal use)

adjust.parameter.count

Adjust count of estimated parameters

Adjust over-dispersion scale or a result value such as effective sample size

collect.model.names

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

MARK model beta parameters

Summary of changes by version

Compute estimates of real parameters

Convert MARK input file to RMark dataframe

Compute estimates of link values

Compute sets of link values for real parameters

convert.link.to.real

Convert link values to 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

add.design.data

Add design data

San Luis Valley mallard data

Removes unused MARK output files

create.model.list

Creates a dataframe of all combinations of parameter specifications

Example data for Closed Robust Design Multistrata

Export capture-history data to MARK .inp format

Computes some derived abundance estimates for POPAN models

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

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

mark.wrapper.parallel

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

Inverse link functions (internal use)

create.mark.mcmc

Create mcmc object for analysis with coda

edwards.eberhardt

Rabbit capture-recapture data

Compute estimates of real parameters with individual and design covariates

White-tailed deer double observer spotlight capture-recapture analysis

Dipper capture-recapture data

Killdeer nest survival example data

deltamethod.special

Compute delta method variance for sum, cumsum, prod and cumprod functions

deriv_inverse.link

Derivatives of inverse of link function (internal use)

Mallard nest survival example

Runs analysis with MARK model using MARK.EXE

make.time.factor

Make time-varying dummy variables from time-varying factor variable

make.mark.model

Create a MARK model for analysis

Print MARK objects

Print MARK list objects

Runs RELEASE for goodness of fit test

Remove mark models from list

Runs a set of MARK models

Provides a summary for the capture histories

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

model.average.list

Compute model averaged estimates of real parameters from a list structure for estimates

Interface to MARK for fitting capture-recapture models

model.average.marklist

Compute model averaged estimates of real parameters

Extract or compute sets of real parameters

extract.indices

Various utility functions

compute.links.from.reals

Compute link values from real parameters

Load external model

Process encounter history dataframe for MARK analysis

make.design.data

Create design dataframes for MARK model specification

merge_design.covariates

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

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

Merge mark model objects and lists of mark model objects

extract.mark.output

Extract results from MARK output file (internal use)

Compute model averaged estimates

read.mark.binary

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

valid.parameters

Determine validity of parameters for a model (internal use)

Runs a previous MARK model with new starting values

Robust design example data

print.summary.mark

Prints summary of MARK model parameters and results

setup.parameters

Setup parameter structure specific to model (internal use)

Salamander occupancy data

An example of the Mulstistrata (multi-state) model in which states are routes taken by migrating fish.

Defines model specific parameters (internal use)

Process release-recapture history data

Variance components estimation

var.components.reml

Variance components estimation using REML or maximum likelihood

Summary of MARK model parameters and results

fill.covariates

Fill covariate entries in MARK design matrix with values

find.covariates

Find covariates in MARK design matrix

Create table of MARK model selection results

Multistrata example data

Split/collapse capture histories

Store models externally or restore to workspace from external storage

Occupancy data for Mahoenui Giant Weta

White-winged dove Jolly-Seber POPAN Analysis Details