INTRODUCTION TO THE EXAMPLES

The following sections how the software can be used on several toy
problems.  These examples are meant to illustrate the features of the
software.  You should note that the models and Markov chain methods
used are not necessarily appropriate for other problems.  To gain a
full understanding of the various possibilities, and their advantages
and disadvantages, you will need to read both the pertinent references
(see Facilities.doc), and the detailed documentation on the various
commands.

The output shown for these examples was obtained by running the
software on our machine, with ">" at the start of a line indicating a
command line that was input.  It is possible (even likely) that your
results will differ, even if you have installed the software
correctly, since small differences in floating point arithmetic can be
magnified into large differences in the course of the simulation.
However, unless one of the simulations became stuck in an isolated
local mode, the final predictions you obtain (eg, from 'net-pred' or
'gp-pred'), and the final distributions of model parameters, should be
close to those reported below.

Some of the examples show the example of "xxx-plt" commands being
piped into a program called "plot".  Any plot program could be used
that reads pairs of numbers from standard input and plots them (in
some cases, a blank line is present to indicate the start of a new
sub-plot).  I use the "xgraph" program written by David Harrison,
which can be obtained from my web page.  If you don't have a plot
program that can be used in this convenient fashion, you can redirect
the output to a file (eg, "net-plt t l log >file") and then read this
file into whatever plotting program you have.  As a last resort, you
can also just look at the numbers in the file yourself.

All the data sets mentioned here are present in directories with names
beginning with "ex", along with the C source of the programs that
generated the data.  The commands given assume that you are in the
directory containing the data.  The command sequences used for each
example are also stored in these directories, in shell files with the
names like 'rcmds.net', 'rcmds.gp', 'bcmds.net', 'bcmds.gp', etc.  The
'ex-mix' and 'ex-ais' directories also contain other command files
used for examples in my papers.

Computation times are given for many of the examples.  These are all
for the current version of the software, run on our computer, which is
an SGI machine with 194 MHz MIPS R10000 processors, running IRIX 6.5.