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&amp;F model <br> lhmax.apf - S-Plus code for auxiliary particle filter for LH model <br> hfmax.call - S-Plus code that calls hfmax.apf and loads data <br> lhmax.call - S-Plus code that calls lhmax.apf and loads data <br> Utilities - S-Plus code with miscellaneous functions used by the .apf pgms <br> est.counts - data file for juvenile and adult data (1996–2001) <br> rbdd.adult - data file for adult returns to Redd Bluff Diversion Dam (1967–2001) <br> 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 <i>N.opt</i>. <br> The degree of kernel smoothing is set by the object <i>discount.opt</i>; it must be between 0 and 1 (values close to 1 are generally preferred; 0.9 is used in the paper).