Exercise 8 example data
Multiple Species Occupancy
Example of Poisson Mark-Resight model
Example of Poisson Mark-Resight model
Robust design salamander occupancy data
Density Estimation with Telemetry
Burnham Live-Dead Model
Multi-scale dynamic occupancy models in RMark
Multi-state occupancy example data
Multi-state Transition Functions
Robust Design occupancy example data
Collect MARK models into a list and optionally construct a table of model
results
MARK model beta parameters
Removes unused MARK output files
Collect names of MARK model objects from list of R objects (internal
function)
San Luis Valley mallard data
Adjust over-dispersion scale or a result value such as effective sample size
Adjust count of estimated parameters
Compute link values from real parameters
Compute estimates of link values
Display PIM for a parameter
Compute design data for a specific parameter in the MARK model (internal
use)
Convert link values to real parameters
Compute estimates of real parameters
Simulated data from Cormack-Jolly-Seber model
Export data and models for import in MARK
Compute estimates of real parameters for multiple covariate values
Load external model
Killdeer nest survival example data
Convert MARK input file to RMark dataframe
Compute delta method variance for sum, cumsum, prod and cumprod functions
Create design dataframes for MARK model specification
Lark Sparrow
Mulstistate Live-Dead Paradise Shelduck Data
Various utility functions
Derivatives of inverse of link function (internal use)
Extract results from MARK output file (internal use)
Inverse link functions (internal use)
Import capture-recapture data sets from space or tab-delimited files
Creates a dataframe of all combinations of parameter specifications
Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
Fill covariate entries in MARK design matrix with values
White-tailed deer double observer spotlight capture-recapture analysis
Add design data
Runs analysis with MARK model using MARK.EXE
Find covariates in MARK design matrix
Summary of changes by version
Runs a set of MARK models
Merge time (occasion) and/or group specific covariates into design data
Dipper capture-recapture data
Rabbit capture-recapture data
Interface to MARK for fitting capture-recapture models
Mallard nest survival example
Constructs and runs a set of MARK models from a dataframe of parameter
specifications
Process encounter history dataframe for MARK analysis
Create table of MARK model selection results
Compute model averaged estimates
Multistrata example data
Merge mark model objects and lists of mark model objects
Strip comments
Summary of MARK model parameters and results
Salamander occupancy data
Compute model averaged estimates of real parameters from a list structure
for estimates
Compute model averaged estimates of real parameters
Compute estimates of real parameters with individual and design covariates
Runs a previous MARK model with new starting values
Reads binary file output from MARK and returns a list of the results
Computes some derived abundance estimates for POPAN models
Create mcmc object for analysis with coda
Process release-recapture history data
Example data for Closed Robust Design Multistrata
Prints summary of MARK model parameters and results
Runs RELEASE for goodness of fit test
Constructs and runs in parallel a set of MARK models from a dataframe of parameter
specifications
Variance components estimation
Variance components estimation using REML or maximum likelihood
Remove mark models from list
Defines model specific parameters (internal use)
An example of the Multistrata (multi-state) model in which states are routes taken by migrating fish.
Setup parameter structure specific to model (internal use)
Compute sets of link values for real parameters
Robust design example data
Export output files for appending into MARK .dbf/.fpt format
Export capture-history data to MARK .inp format
Extract or compute sets of real parameters
Determine validity of parameters for a model (internal use)
Provides a summary for the capture histories
Create a MARK model for analysis
Occupancy data for Mahoenui Giant Weta
White-winged dove Jolly-Seber POPAN Analysis Details
Print MARK list objects
Split/collapse capture histories
Store models externally or restore to workspace from external storage
Print MARK objects
Make time-varying dummy variables from time-varying factor variable
Example of Immigration-Emigration LogitNormal Mark-Resight model
A beginners introduction and guide to RMark
Black duck known fate data
Example of LogitNormal Mark-Resight model
Exercise 7 example data
Convert Multistate data for POPAN-style abundance estimation
Truncate capture histories for multi-state models