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marked (version 1.2.8)

Mark-Recapture Analysis for Survival and Abundance Estimation

Description

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.

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Install

install.packages('marked')

Monthly Downloads

1,373

Version

1.2.8

License

GPL (>= 2)

Maintainer

Last Published

October 19th, 2023

Functions in marked (1.2.8)

compute_matrices

Compute HMM matrices

HMM Transition matrix functions

convert.link.to.real

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.fixed.matrix

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

function.wrapper

Utility extract functions

deriv_inverse.link

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

make.design.data

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_design.covariates

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.model.admb

Mixed effect model contstruction

mvms_design_data

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

Simulates data from Hidden Markov Model

valid.parameters

Determine validity of parameters for a model (internal use)

Defines model specific parameters (internal use)

setup.parameters

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

R_HMMLikelihood

Hidden Markov Model Functions

Various utility parameter summary functions

Accumulates common capture history values

Paradise_shelduck

Mulstistate Live-Dead Paradise Shelduck Data