RMark

A beginners introduction and guide to RMark

Black duck known fate data

Burnham Live-Dead Model

Density Estimation with Telemetry

Exercise 7 example data

Exercise 8 example data

Example of Immigration-Emigration LogitNormal Mark-Resight model

Example of LogitNormal Mark-Resight model

Convert Multistate data for POPAN-style abundance estimation

Truncate capture histories for multi-state models

Multiple Species Occupancy

Multi-state occupancy example data

Display PIM for a parameter

Mulstistate Live-Dead Paradise Shelduck 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

Robust design salamander occupancy data

Multi-state Transition Functions

Summary of changes by version

Add design data

Adjust count of estimated parameters

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

San Luis Valley mallard data

Removes unused MARK output files

MARK model beta parameters

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

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

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

Compute estimates of link values

Compute link values from real parameters

Compute estimates of real parameters

Convert MARK input file to RMark dataframe

Convert link values to real parameters

Compute estimates of real parameters for multiple covariate values

Example data for Closed Robust Design Multistrata

Create mcmc object for analysis with coda

Creates a dataframe of all combinations of parameter specifications

White-tailed deer double observer spotlight capture-recapture analysis

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

Derivatives of inverse of link function (internal use)

Dipper capture-recapture data

Rabbit capture-recapture data

Simulated data from Cormack-Jolly-Seber model

Export data and models for import in MARK

Export capture-history data to MARK .inp format

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

Various utility functions

Extract results from MARK output file (internal use)

Fill covariate entries in MARK design matrix with values

Find covariates in MARK design matrix

Compute sets of link values for real parameters

Extract or compute sets of real parameters

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

Inverse link functions (internal use)

Killdeer nest survival example data

Lark Sparrow

Load external model

Create design dataframes for MARK model specification

Create a MARK model for analysis

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

Mallard nest survival example

Interface to MARK for fitting capture-recapture models

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

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

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

Merge mark model objects and lists of mark model objects

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

Compute model averaged estimates

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

Compute model averaged estimates of real parameters

Create table of MARK model selection results

Multistrata example data

Computes some derived abundance estimates for POPAN models

Compute estimates of real parameters with individual and design covariates

Print MARK objects

Print MARK list objects

Prints summary of MARK model parameters and results

Process release-recapture history data

Process encounter history dataframe for MARK analysis

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

Runs RELEASE for goodness of fit test

Remove mark models from list

Runs a previous MARK model with new starting values

Robust design example data

Runs analysis with MARK model using MARK.EXE

Runs a set of MARK models

Salamander occupancy data

Defines model specific parameters (internal use)

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.

Split/collapse capture histories

Store models externally or restore to workspace from external storage

Strip comments

Summary of MARK model parameters and results

Provides a summary for the capture histories

Determine validity of parameters for a model (internal use)

Variance components estimation

Variance components estimation using REML or maximum likelihood

Occupancy data for Mahoenui Giant Weta

White-winged dove Jolly-Seber POPAN Analysis Details