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