Mark-Recapture Analysis for Survival and Abundance Estimation
Compute variance-covariance matrix for fitted CJS model
Computes starting values for CJS p and Phi parameters
Likelihood function for Cormack-Jolly-Seber model
Fitting function for CJS models
HMM Initial state distribution functions
HMM Transition matrix functions
Fitting function for CJS models
Extract coefficients
Compute HMM matrices
Computes backward probabilities
Accumulates common capture history values
Compute estimates of real parameters
Convert link values to real parameters
Creates a design matrix for a parameter
Creates a dataframe with all the design data for a particular paramete...
Create parameters with fixed matrix
Creates a 0/1 vector for real parameters with sin link
Capture-recapture model fitting function
Automation of model runs
Derivatives of inverse of link function (internal use)
Create expanded state-dependent observation matrix for HMM from HSMM
Fixing real parameters in crm models
Utility extract functions
Global decoding of HMM
HMM computation demo functions
Hidden Markov Model likelihood functions
Compute transition matrix for HMM from HSMM
Setup fixed values for pi in design data
Inverse link functions (internal use)
Accumulates common capture history values
Compute variance-covariance matrix for fitted JS model
Likelihood function for Jolly-Seber model using Schwarz-Arnason POPAN ...
Fitting function for Jolly-Seber model using Schwarz-Arnason POPAN for...
Local decoding of HMM
Create design dataframes for crm
Merge time (occasion) and/or group specific covariates into design dat...
Mixed effect model contstruction
Fitting function for Multistate CJS models
Fitting function for Multistate CJS models with TMB
Fitting function for Multistate CJS live-dead models with TMB
Multivariate Multistate (mvms) Design Data
HMM Observation Probability matrix functions
Fitting function for Multivariate Multistate CJS with uncertainty mode...
TMB version: Fitting function for Multivariate Multistate CJS with unc...
Compute 1 to k-step transition proportions
Various utility parameter summary functions
Compute estimates of real parameters
Print model results
Print model table from model list
Perform MCMC analysis of a CJS model
Mixed effect model formula parserParses a mixed effect model in the lm...
Process release-recapture history data
Process encounter history dataframe for MARK analysis
Hidden Markov Model Functions
Various utility functions
Set fixed real parameter values in ddl
Set initial values
Multivariate Multistate (mvms) Specification
Scaling functions
Defines model specific parameters (internal use)
Setup parameter structure specific to model (internal use)
ADMB setup
TMB setup
Simulates data from Hidden Markov Model
Fitting function for Multistate CJS live-dead models with TMB
Split/collapse capture histories
Determine validity of parameters for a model (internal use)
Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.