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RMark (version 2.1.12)

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 (http://www.phidot.org/software/mark/downloads/) but is not open source.

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Version

Install

install.packages('RMark')

Monthly Downloads

865

Version

2.1.12

License

GPL (>= 2)

Maintainer

Jeff Laake

Last Published

March 15th, 2015

Functions in RMark (2.1.12)

MARK model beta parameters

Example of LogitNormal Mark-Resight model

Exercise 8 example data

IELogitNormalMR

Example of Immigration-Emigration LogitNormal Mark-Resight model

Simulated data from Cormack-Jolly-Seber model

deriv_inverse.link

Derivatives of inverse of link function (internal use)

San Luis Valley mallard data

Compute sets of link values for real parameters

Example of Poisson Mark-Resight model

Export capture-history data to MARK .inp format

compute.design.data

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

create.model.list

Creates a dataframe of all combinations of parameter specifications

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

NicholsMSOccupancy

Multi-state occupancy example data

edwards.eberhardt

Rabbit capture-recapture data

Compute estimates of real parameters

extract.indices

Various utility functions

ABeginnersGuide

A beginners introduction and guide to RMark

Black duck known fate data

create.mark.mcmc

Create mcmc object for analysis with coda

make.time.factor

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

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

Convert Multistate data for POPAN-style abundance estimation

collect.model.names

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

Display PIM for a parameter

Remove mark models from list

Inverse link functions (internal use)

fill.covariates

Fill covariate entries in MARK design matrix with values

White-tailed deer double observer spotlight capture-recapture analysis

find.covariates

Find covariates in MARK design matrix

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

setup.parameters

Setup parameter structure specific to model (internal use)

Robust design salamander occupancy data

extract.mark.output

Extract results from MARK output file (internal use)

Exercise 7 example data

print.summary.mark

Prints summary of MARK model parameters and results

Summary of MARK model parameters and results

Runs analysis with MARK model using MARK.EXE

convert.link.to.real

Convert link values to real parameters

Create table of MARK model selection results

Variance components estimation

var.components.reml

Variance components estimation using REML or maximum likelihood

Provides a summary for the capture histories

TransitionMatrix

Multi-state Transition Functions

Example data for Closed Robust Design Multistrata

valid.parameters

Determine validity of parameters for a model (internal use)

Dipper capture-recapture data

Split/collapse capture histories

make.mark.model

Create a MARK model for analysis

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

make.design.data

Create design dataframes for MARK model specification

Store models externally or restore to workspace from external storage

Load external model

Interface to MARK for fitting capture-recapture models

adjust.parameter.count

Adjust count of estimated parameters

Robust Design occupancy example data

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

model.average.marklist

Compute model averaged estimates of real parameters

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

Mallard nest survival example

Computes some derived abundance estimates for POPAN models

Multistrata example data

Process encounter history dataframe for MARK analysis

read.mark.binary

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

Summary of changes by version

Example of Poisson Mark-Resight model

Print MARK list objects

Occupancy data for Mahoenui Giant Weta

Runs RELEASE for goodness of fit test

Runs a previous MARK model with new starting values

Salamander occupancy data

Export data and models for import in MARK

Extract or compute sets of real parameters

Runs a set of MARK models

Killdeer nest survival example data

compute.links.from.reals

Compute link values from real parameters

deltamethod.special

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

Compute model averaged estimates

model.average.list

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

Defines model specific parameters (internal use)

White-winged dove Jolly-Seber POPAN Analysis Details

Robust design example data

Compute estimates of link values

covariate.predictions

Compute estimates of real parameters for multiple covariate values

Merge mark model objects and lists of mark model objects

Print MARK objects

add.design.data

Add design data

Removes unused MARK output files

Convert MARK input file to RMark dataframe

merge_design.covariates

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