Jonas Knape and Perry de Valpine. 2012. Fitting complex population models by combining particle filters with Markov chain Monte Carlo. Ecology 93:256–263.

Supplement

R code for fitting the random-walk state space model using particle filter MCMC.
Ecological Archives E093-025-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

Jonas Knape
Dept. of Environmental Science, Policy and Management
137 Mulford Hall #3114
University of California at Berkeley
Berkeley, CA 94720
USA
Email: jknape@berkeley.edu

Perry de Valpine
Dept. of Environmental Science, Policy and Management
137 Mulford Hall #3114
University of California at Berkeley
Berkeley, CA 94720
USA.

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.