K. B. Newman, S. T. Buckland, S. T. Lindley, L. Thomas , and C. Fernández. 2006. Hidden process models for animal population dynamics. Ecological Applications 16:74–86.


Supplement

S-Plus code used in paper to fit life history (LH) and Hallock and Fisher (HF) hidden process models, along with data files.
Ecological Archives
A016-006-S1
.

Copyright


Authors
File list (downloads)
Description


Author(s)

Ken B. Newman
School of Mathematics and Statistics
University of St. Andrews
St. Andrews, KY16 9LZ, Scotland
email: ken@mcs.st-and.ac.uk

Steve T. Buckland
School of Mathematics and Statistics
University of St. Andrews
St. Andrews, KY16 9LZ, Scotland
email: steve@mcs.st-and.ac.uk

Steven T. Lindley
National Marine Fisheries Service
Santa Cruz Laboratory, 110 Shaffer Road
Santa Cruz, CA 95060 USA
email: steve.lindley@noaa.gov

Len Thomas
School of Mathematics and Statistics
University of St. Andrews
St. Andrews, KY16 9LZ, Scotland
email: len@mcs.st-and.ac.uk

Carmen Fernandez
Department of Mathematics and Statistics
Fylde College, Lancaster University
Lancaster, England
email: c.fernandez@lancaster.ac.uk


File list

hfmax.apf - S-Plus code for auxiliary particle filter for H&F model
lhmax.apf - S-Plus code for auxiliary particle filter for LH model
hfmax.call - S-Plus code that calls hfmax.apf and loads data
lhmax.call - S-Plus code that calls lhmax.apf and loads data
Utilities - S-Plus code with miscellaneous functions used by the .apf pgms
est.counts - data file for juvenile and adult data (1996–2001)
rbdd.adult - data file for adult returns to Redd Bluff Diversion Dam (1967–2001)
hpmall.tar - tar file of all the above files

Description

All the above files can be put into the default working directory for S-Plus (Version 6.1.2 Release 2 for Linux 2.2.12: 2002) and then sourcing the .call files will run the .apf files. Alternate storage locations can be used but then the .call files will need to be edited for the alternate locations.

Alternate output locations can be created, also, by editing the write() lines in hfmax.apf and lhmax.apf. These files currently assume that output directories named HFOUT and LHOUT exist.

The number of particles generated is set by the object labelled N.opt.
The degree of kernel smoothing is set by the object discount.opt; it must be between 0 and 1 (values close to 1 are generally preferred; 0.9 is used in the paper).



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