Various utility parameter summary functions
Mulstistate Live-Dead Paradise Shelduck Data
Hidden Markov Model likelihood functions
Compute HMM matrices
Automation of model runs
Compute estimates of real parameters
Hidden Markov Model Functions
Computes starting values for CJS p and Phi parameters
Creates a design matrix for a parameter
Compute variance-covariance matrix for fitted CJS model
Convert link values to real parameters
Global decoding of HMM
Fitting function for CJS models
Accumulates common capture history values
HMM computation demo functions
Extract coefficients
Derivatives of inverse of link function (internal use)
Creates a dataframe with all the design data for a particular parameter in a
crm model
Compute transition matrix for HMM from HSMM
Likelihood function for Jolly-Seber model using Schwarz-Arnason POPAN
formulation
Fixing real parameters in crm models
Create parameters with fixed matrix
Utility extract functions
Accumulates common capture history values
Creates a 0/1 vector for real parameters with sin link
Capture-recapture model fitting function
Compute variance-covariance matrix for fitted JS model
Local decoding of HMM
TMB version: Fitting function for Multivariate Multistate CJS with uncertainty models
Setup fixed values for pi in design data
HMM Initial state distribution functions
HMM Transition matrix functions
Dipper capture-recapture data
Create expanded state-dependent observation matrix for HMM from HSMM
HMM Observation Probability matrix functions
Compute 1 to k-step transition proportions
Inverse link functions (internal use)
Fitting function for Jolly-Seber model using Schwarz-Arnason POPAN
formulation
Mixed effect model contstruction
Create design dataframes for crm
Process encounter history dataframe for MARK analysis
Fitting function for Multivariate Multistate CJS with uncertainty models
Set initial values
Scaling functions
Various utility functions
Fitting function for Multistate CJS live-dead models with TMB
Process release-recapture history data
Mixed effect model formula parser
Parses a mixed effect model in the lme4 structure of ~fixed +(re1|g1) +...+(ren|gn)
An example of the Mulstistrata (multi-state) model in which states are routes taken by migrating fish.
Fitting function for Multistate CJS models with TMB
Merge time (occasion) and/or group specific covariates into design data
Multivariate State example data
Fitting function for Multistate CJS models
Print model table from model list
Set fixed real parameter values in ddl
Multivariate Multistate (mvms) Specification
Split/collapse capture histories
Defines model specific parameters (internal use)
Setup parameter structure specific to model (internal use)
ADMB setup
Perform MCMC analysis of a CJS model
Tag loss example
Determine validity of parameters for a model (internal use)
Compute estimates of real parameters
Multivariate Multistate (mvms) Design Data
Multistrata example data
Print model results
TMB setup
Simulates data from Hidden Markov Model
Likelihood function for Cormack-Jolly-Seber model
Computes backward probabilities
Fitting function for CJS models