This directory contains code to reproduce the PMCMC example.

The system for this example is set up for potential distributed computing,
but the code provided here runs all cases in serial.

The files for running the cases are as follows.  These use each other in the
order listed.

SVexample_run_all_replicates.R: Source this file from R to run everything

SVexample_run_replicate.R: This contains an R function to run one replicate,
including all combinations of number of particles, M, and proposal standard
deviation factor, h.  It writes configuration files and calls the next file
as a script via system().

SVexample_setup_and_run_one_case.R: This is designed to be called as a
script from the command line.  It reads a configuration file and source()s
the next file.  (One might need to do "chmod u+x
SVexample_setup_and_run_one_case.R" before using this.)

SVexample_run_one_case.R: This contains the core code for creating the model
and algorithm and running them.  This is called via source() from
SVexample_setup_and_run_one_case.R.

The files for processing results and creating figure are:

SVexample_make_traceplot.R: This uses only the first replicate

SVexample_process_results.R: This creates the figure showing ESS and
efficiency comparisons.
