James R. Thomson, Wim J. Kimmerer, Larry R. Brown, Ken B. Newman, Ralph Mac Nally, William A. Bennett, Frederick Feyrer, and Erica Fleishman. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications 20:1431–1448.


Supplement

WinBUGS and R code to fit change point and variable selection models.
Ecological Archives
A020-051-S1
.

Copyright


Authors
File list (downloads)
Description


Author(s)

Jim Thomson
Australian Centre for Biodiversity, School of Biological Sciences
Monash University
Melbourne 3800
Australia
E-mail: jim.thomson@sci.monash.au


File list

trend model with changepoints.txt  - WinBUGS model file for trend model with change points
R code to fit trend model with change points.R  - R script for fitting trend model via R2WinBUGS
varselect model.txt  - WinBUGS model file for non-linear variable selection model
R code to fit variable selection model.R  - R script for fitting variable selection model via R2WinBUGS
CCCP model.txt  - WinBUGS model file for covariate conditioned change point model
R code to fit cccp model.R  - R script for fitting covariate conditioned change point model via R2WinBUGS
multispecies changepoint.txt  - WinBUGS model file for multi-species covariate conditioned change point model
R code to fit multispecies cccp model.R  - R script for fitting multi-species covariate conditioned change point model via R2WinBUGS
Data.zip  - Data saved as R objects to demonstrate use of R scripts and WinBUGS models


Download all files.zip 

Description

The .txt files are WinBUGS model codes for the models described in the paper. These models require the reversible "jump" add-on for WinBUGS (available from WinBUGS development website). The R scripts can be used to generate required data files and run the WinBUGS models from R. Data.zip contains example input data for all models. The R scripts require all files to be in the R working directory and the R2WinBUGS package must be installed.


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