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RMark (version 2.1.1)

R Code for MARK Analysis

Description

This package provides an interface to the software package MARK developed by Gary White. MARK is freely available at (http://www.phidot.org/software/mark/download/) but is not open source.

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Version

Install

install.packages('RMark')

Monthly Downloads

1,273

Version

2.1.1

License

GPL (>= 2)

Maintainer

Jeff Laake

Last Published

May 5th, 2012

Functions in RMark (2.1.1)

compute.links.from.reals

Compute link values from real parameters

Display PIM for a parameter

NicholsMSOccupancy

Multi-state occupancy example data

create.model.list

Creates a dataframe of all combinations of parameter specifications

Black duck known fate data

Exercise 7 example data

mark.wrapper.parallel

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

adjust.parameter.count

Adjust count of estimated parameters

Dipper capture-recapture data

Export data and models for import in MARK

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

Mallard nest survival example

fill.covariates

Fill covariate entries in MARK design matrix with values

Compute estimates of link values

Convert MARK input file to RMark dataframe

Runs a set of MARK models

Robust Design occupancy example data

Compute model averaged estimates

Example of Poisson Mark-Resight model

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

Summary of MARK model parameters and results

Export capture-history data to MARK .inp format

Example of LogitNormal Mark-Resight model

make.time.factor

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

Interface to MARK for fitting capture-recapture models

IELogitNormalMR

Example of Immigration-Emigration LogitNormal Mark-Resight model

extract.indices

Various utility functions

Merge mark model objects and lists of mark model objects

Salamander occupancy data

Simulated data from Cormack-Jolly-Seber model

read.mark.binary

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

Multistrata example data

Example data for Closed Robust Design Multistrata

Robust design salamander occupancy data

Runs a previous MARK model with new starting values

TransitionMatrix

Creates a transition matrix of movement parameters for a multi-state(strata) model

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

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

deriv_inverse.link

Derivatives of inverse of link function (internal use)

merge_design.covariates

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

Compute sets of link values for real parameters

model.average.marklist

Compute model averaged estimates of real parameters

Process encounter history dataframe for MARK analysis

extract.mark.output

Extract results from MARK output file (internal use)

valid.parameters

Determine validity of parameters for a model (internal use)

Example of Poisson Mark-Resight model

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

collect.model.names

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

var.components.reml

Variance components estimation using REML or maximum likelihood

Runs analysis with MARK model using MARK.EXE

Killdeer nest survival example data

edwards.eberhardt

Rabbit capture-recapture data

Provides a summary for the capture histories

Print MARK objects

Occupancy data for Mahoenui Giant Weta

ABeginnersGuide

A beginners introduction and guide to RMark

Compute estimates of real parameters

Load external model

San Luis Valley mallard data

Inverse link functions (internal use)

convert.link.to.real

Convert link values to real parameters

Extract or compute sets of real parameters

Convert Multistate data for POPAN-style abundance estimation

covariate.predictions

Compute estimates of real parameters for multiple covariate values

Exercise 8 example data

make.design.data

Create design dataframes for MARK model specification

create.mark.mcmc

Create mcmc object for analysis with coda

Defines model specific parameters (internal use)

model.average.list

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

compute.design.data

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

Robust design example data

find.covariates

Find covariates in MARK design matrix

Remove mark models from list

Variance components estimation

Computes some derived abundance estimates for POPAN models

White-tailed deer double observer spotlight capture-recapture analysis

Summary of changes by version

Create table of MARK model selection results

add.design.data

Add design data

Removes unused MARK output files

Runs RELEASE for goodness of fit test

make.mark.model

Create a MARK model for analysis

setup.parameters

Setup parameter structure specific to model (internal use)

Truncate capture histories for multi-state models

deltamethod.special

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

Split/collapse capture histories

Store models externally or restore to workspace from external storage

MARK model beta parameters

Print MARK list objects

#' Burnham Live-Dead Model

print.summary.mark

Prints summary of MARK model parameters and results

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

Process release-recapture history data

White-winged dove Jolly-Seber POPAN Analysis Details

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