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.
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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
Mark L. Taper
Ecology Department, Montana State University
301 Lewis Hall, Bozeman, Montana
Department of Fish and Wildlife Resources and Department of Statistics
University of Idaho, Moscow, Idaho
Subhash R. Lele
Department of Mathematical and Statistical Sciences
University of Alberta, Edmonton, Alberta,
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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