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

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 output 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 '', '', '', '', etc.
Some of these 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 the system described
in Ex-system.doc, except for the examples in Ex-dist-g.doc and
Ex-dist-f.doc, which I've left with times for an older version of the
software, run on a 550 MHz Pentium III.