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RMark (version 2.2.0)

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

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Version

Install

install.packages('RMark')

Monthly Downloads

12,783

Version

2.2.0

License

GPL (>= 2)

Maintainer

Jeff Laake

Last Published

June 23rd, 2016

Functions in RMark (2.2.0)

San Luis Valley mallard data

Black duck known fate data

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

MARK model beta parameters

ABeginnersGuide

A beginners introduction and guide to RMark

Removes unused MARK output files

add.design.data

Add design data

collect.model.names

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

adjust.parameter.count

Adjust count of estimated parameters

#' Burnham Live-Dead Model

Compute estimates of link values

Compute estimates of real parameters

Example data for Closed Robust Design Multistrata

create.mark.mcmc

Create mcmc object for analysis with coda

convert.link.to.real

Convert link values to real parameters

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)

Convert MARK input file to RMark dataframe

covariate.predictions

Compute estimates of real parameters for multiple covariate values

compute.links.from.reals

Compute link values from real parameters

White-tailed deer double observer spotlight capture-recapture analysis

create.model.list

Creates a dataframe of all combinations of parameter specifications

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

IELogitNormalMR

Example of Immigration-Emigration LogitNormal Mark-Resight model

Inverse link functions (internal use)

Simulated data from Cormack-Jolly-Seber model

Killdeer nest survival example data

Export capture-history data to MARK .inp format

Compute sets of link values for real parameters

Extract or compute sets of real parameters

Interface to MARK for fitting capture-recapture models

print.summary.mark

Prints summary of MARK model parameters and results

Mallard nest survival example

Process release-recapture history data

Exercise 8 example data

edwards.eberhardt

Rabbit capture-recapture data

Export data and models for import in MARK

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

Load external model

Exercise 7 example data

Dipper capture-recapture data

find.covariates

Find covariates in MARK design matrix

fill.covariates

Fill covariate entries in MARK design matrix with values

Example of LogitNormal Mark-Resight model

make.design.data

Create design dataframes for MARK model specification

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

merge_design.covariates

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

Print MARK objects

Print MARK list objects

make.mark.model

Create a MARK model for analysis

Convert Multistate data for POPAN-style abundance estimation

make.time.factor

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

Create table of MARK model selection results

Multistrata example data

Truncate capture histories for multi-state models

Runs a previous MARK model with new starting values

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

Example of Poisson Mark-Resight model

Example of Poisson Mark-Resight model

Runs analysis with MARK model using MARK.EXE

Runs a set of MARK models

Process encounter history dataframe for MARK analysis

deltamethod.special

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

Robust Design occupancy example data

deriv_inverse.link

Derivatives of inverse of link function (internal use)

extract.indices

Various utility functions

extract.mark.output

Extract results from MARK output file (internal use)

Merge mark model objects and lists of mark model objects

Compute model averaged estimates

Computes some derived abundance estimates for POPAN models

Robust design salamander occupancy data

Compute estimates of real parameters with individual and design covariates

read.mark.binary

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

setup.parameters

Setup parameter structure specific to model (internal use)

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

valid.parameters

Determine validity of parameters for a model (internal use)

Variance components estimation

var.components.reml

Variance components estimation using REML or maximum likelihood

Summary of MARK model parameters and results

Provides a summary for the capture histories

Occupancy data for Mahoenui Giant Weta

TransitionMatrix

Multi-state Transition Functions

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

mark.wrapper.parallel

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

NicholsMSOccupancy

Multi-state occupancy example data

Display PIM for a parameter

Runs RELEASE for goodness of fit test

Remove mark models from list

Defines model specific parameters (internal use)

Salamander occupancy data

Split/collapse capture histories

Store models externally or restore to workspace from external storage

Robust design example data

White-winged dove Jolly-Seber POPAN Analysis Details

Summary of changes by version