The BUGS software

BUGS Version 0.6 is a program for carrying out Gibbs sampling in complex models. Please note it is not being further developed – we now concentrate on the WinBUGS package.

What do you Get?

BUGS is distributed as compiled code suitable for a variety of platforms. UNIX versions are run from one of two shell scripts: bugs or backbugs. The DOS version is run from one of two batch files: bugs.bat or backbugs.bat.

BUGS 0.6 is currently available for the following platforms.

Program    Platform    Version
prog06.sparc    SUN Sparc    0.60
prog06.exe    PCs running DOS (32 Bit)    0.60
prog06.sgi    SGI    0.60
prog06.linux    LINUX    0.60
See `details of different versions’ for improvements and known bugs.

We hope to have a version for IBM RS6000 available soon.

WARNING – the versions of BUGS06 for linux and sgi machines has not undergone rigorous testing and may be liable to crash. Any feedback on these versions will be greatly appreciated.

The programs are available in the following files, where XYZ stands for the relevant platform (i.e. sparc, linux and so on)

File    Contents when Unpacked    Type    Description
/unix/prog06.XYZ.tar.z    bugs06.XYZ    binary    Version 0.60 for platform XYZ
bugs    ascii    shell script
backbugs    ascii    shell script
/dos/prog06.exe    bugs06.exe    binary    Version 0.60 for DOS
go32.exe    binary    DOS extender
bugs.bat    ascii    shell script
backbugs.bat    ascii    shell script
When taking any of our programs, please make sure you leave a full e-mail address.

Obtaining files for UNIX systems

Directly from the Web page

Go to the download page and click on the relevant icon. A window will then appear giving you the option to save the file to a selected directory.

Unpacking files

You will need to uncompress and untar the files by typing

• uncompress prog06.XYZ.tar.Z
• tar xvpf prog06.XYZ.tar

which will unpack the files into your current directory. You should then move these files to a directory which is on your path (say the /bin directory), or add the current directory to your path if it is not on there already.

[Note: If you want to try running BUGS as soon as you have unpacked it and modified your path (i.e. without having logged out first), remember to first type

rehash

This recomputes the internal hash table of the contents of directories listed in the path variable to account for the new files you have just added.]

Obtaining files for DOS systems

Directly from the Web page

Go to the download page and click on the relevant icon. A window will then appear giving you the option to save the file to a selected directory.

 

Unpacking files

Unpack the file by typing

prog06.exe -o -d  <return>

In some window systems it may be possible unpack the file by simply trying to open it. The files bugs06.exe, go32.exe, bugs.bat and backbugs.bat will be placed in your current directory. Either add this directory to your path by editing your AUTOEXEC.BAT file, or move these files to a directory which is already on your path.

NOTE: You will need the HIMEM.SYS software driver to run BUGS – check you have this by looking for the line

DEVICE=C:\DOS\HIMEM.SYS

in your CONFIG.SYS file. You will also need a maths co-processor.

Details of Versions

Changes from 0.51
The adaptive rejection sampling routine has been changed in the hope of avoiding the crashes that have occurred. However, this may have made it slower.
A `checkpoint’ command now exists to save people wasting a whole run if a crash occurs. If you want to save the run every 1000 iterations, type checkpoint(1000) then every 1000 iterations BUGS will
write to “bugs.res” the current parameter values
if anything is being monitored, write sequentially to “bugs.sif” (an `ind’ file) and “bugs.sof” (an `out’ file)
“bugs.res” can be used as an initial value file for restarting a run.
A general Metropolis-within-Gibbs routine is now used for non-log-concave sampling. This uses a simple histogram- based proposal distribution, and therefore any parameter that requires Metropolis sampling *must* have bounded range, which is best set up using the I( , ) construct on the prior distribution. This is best adapted to as narrow a range as possible to bound the posterior distribution. The default number of bins in the histogram is 32, but this can be changed within the bugs script.
Non-integer r and n can be used in binomial sampling.
Known bugs in Version 0.603
The multivariate normal sampler has a bug in it. Users are advised to use Version 0.5 for MVN problems.
The loggam, logfact functions give wrong answers (ie correct answers -.918)
The probit function does not work (as a link it’s fine)

Documentation

Click here to obtain documentation for BUGS.

The documentation for BUGS consists of a basic manual for Version 0.5 and an Addendum for Version 0.6. The CODA documentation also comes in two parts: a manual for Version 0.3 and an Addendum for Version 0.4. The Examples have two full detailed manuals.

All the above documentation is available as postscript files. There is a README file on our Web site which contains summaries of the files available and details of how to obtain them.

On page 68 of BUGS 0.5 Examples volume 1 (version i)” manual, Boch, R. D. and Aitkin, M. (1981) and Boch, R. D. and Lieberman, M. (1970) should be Bock, R. D. and Aitkin, M. (1981) and Bock, R. D. and Lieberman, M. (1970)

The missing reference to Goldstein et al (1993) is `H Goldstein and J Rasbash and M Yang and G Woodhouse and H Pan and D Nuttal, “A multilevel analysis of school examination results”, 1993, Oxford Review of Education,19,425–433′.

Examples
Click here to obtain supporting code for the BUGS examples, for either UNIX or DOS systems.

This supporting code supplies all the files needed for the examples in the two Examples manuals (see above). There is a README file on our web site which contain summaries of the files available and details of how to obtain them.