Supplement 1. R code for fitting the random-walk state-space model using particle filter MCMC.

Name: Supplement 1. R code for fitting the random-walk state-space model using particle filter MCMC.
Published: 2016-08-09T11:35:44+00:00
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: Markov chain Monte Carlo (MCMC), particle filter, state-space models, population dynamics, observation error, Environmental Science, Ecology

dataset

posted on 2016-08-09, 11:35 authored by Jonas Knape, Perry de Valpine

File List

adaptiveMH.r (md5: 1c7f3697e28dca0aceda63360930e29f)
adaptiveMHfuns.r (md5: cabc33a60ab779b954d853816c9e3cce)
PF.r (md5: eff6f6611833c86c1d1a8e8135af7e04)

Description

adaptiveMH.r – Contains a script for fitting a random-walk model with drift for Kangaroo population dynamics on the log-scale using particle filtering Metropolis Hastings with an initial adaptive phase.

adaptiveMHfuns.r – Contains functions that are used for estimating and handling the normal mixture proposals.

PF.r – Contains functions that perform the particle filtering and define the model.