R Code for Mark Analysis
Convert Multistate data for POPAN-style abundance estimation
Process release-recapture history data
Process encounter history dataframe for MARK analysis
Multi-scale dynamic occupancy models in RMark
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
Runs analysis with MARK model using MARK.EXE
Runs a set of MARK models
Defines model specific parameters (internal use)
Setup parameter structure specific to model (internal use)
An example of the Multistrata (multi-state) model in which states are ...
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
Multi-state Transition Functions
Determine validity of parameters for a model (internal use)
Variance components estimation
Variance components estimation using REML or maximum likelihood
Summary of changes by version
White-winged dove Jolly-Seber POPAN Analysis Details
Truncate capture histories for multi-state models
Display PIM for a parameter
Computes some derived abundance estimates for POPAN models
Compute estimates of real parameters with individual and design covari...
Print MARK objects
Print MARK list objects
Prints summary of MARK model parameters and results
A beginners introduction and guide to RMark
Add design data
Adjust count of estimated parameters
Adjust over-dispersion scale or a result value such as effective sampl...
Burnham Live-Dead Model
Removes unused MARK output files
MARK model beta parameters
Collect names of MARK model objects from list of R objects (internal f...
Collect MARK models into a list and optionally construct a table of mo...
Compute design data for a specific parameter in the MARK model (intern...
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
Create mcmc object for analysis with coda
Creates a dataframe of all combinations of parameter specifications
Compute delta method variance for sum, cumsum, prod and cumprod functi...
Derivatives of inverse of link function (internal use)
Export capture-history data to MARK .inp format
Export data and models for import in MARK
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)
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
Interface to MARK for fitting capture-recapture models
Constructs and runs in parallel a set of MARK models from a dataframe ...
Constructs and runs a set of MARK models from a dataframe of parameter...
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 dat...
Compute model averaged estimates of real parameters from a list struct...
Compute model averaged estimates of real parameters
Compute model averaged estimates
Create table of MARK model selection results
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.