José Miguel Ponciano, Mark L. Taper, Brian Dennis, and Subhash R. Lele. 2009. Hierarchical models in ecology: confidence intervals, hypothesis testing, and model selection using data cloning. Ecology 90:356–362.


Supplement

R program illustrating the calculations needed to construct a profile likelihood for one of the Stochastic Beverton-Holt state space model parameters. Ecological Archives E090-027-S1.


Authors
File list (downloads)
Description


Author(s)

José Miguel Ponciano Castellanos
Centro de Investigación en Matemáticas CIMAT A.C.
Calle Jalisco s/n. Col. Valenciana
C.P. 36000 A.P. 402,
Guanajuato, Guanajuato, MEXICO
E-mail: ponciano@cimat.mx

Mark L. Taper
Ecology Department, Montana State University
301 Lewis Hall, Bozeman, Montana
59717-3460
USA
E-mail: taper@rapid.msu.montana.edu

Brian Dennis
Department of Fish and Wildlife Resources and Department of Statistics 
University of Idaho, Moscow, Idaho
83844-1136
USA
E-mail: brian@uidaho.edu

Subhash R. Lele
Department of Mathematical and Statistical Sciences
University of Alberta, Edmonton, Alberta,
T6G2G1,
Canada
E-mail: slele@ualberta.ca


File list

SBHPL.R

Description

SBHPLR is a program written in R to calculate the profile likelihood for the parameter lambda of the Stochastic Beverton Holt state-space model as described in the main text. In this program, the necessary MCMC calculations are carried by calling and running the software WinBugs from R using the package BRUGS freely available at <http://www.r-project.org>. Previous installation of WinBugs and BRUGS is required to run this code. Detailed instructions on how to use this program are listed as comments in the file header. The Data Cloning Profile Likelihood (DCPL) algorithm presented in this program is described in the original paper and the proof of why it works can be read in Appendix A.


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