Supplement 1. S-Plus code used to fit life history (LH) and Hallock and Fisher (HF) hidden process models, along with data files.

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).