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ESS[BUGS] was designed for use with BUGS software. It was developed by
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Rodney A. Sparapani and has some similarities with ESS[SAS].
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ESS facilitates BUGS batch with ESS[BUGS], the mode for files with the .bug
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extension. ESS provides 5 features. First, BUGS syntax is described to allow
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for proper fontification of statements, distributions, functions, commands and
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comments in BUGS model files, command files and log files. Second,
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ESS creates templates for the command file from the model file so that
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a BUGS batch process can be defined by a single file. Third, ESS
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provides a BUGS batch script that allows ESS to set BUGS batch
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parameters. Fourth, key sequences are defined to create a command
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file and submit a BUGS batch process. Lastly, interactive submission of BUGS
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commands is also supported.
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@comment node-name, next, previous, up
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@node ESS(BUGS)--Model files, ESS(BUGS)--Command files, ESS for BUGS, ESS for BUGS
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@section ESS[BUGS]--Model files
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Model files (with the .bug extension) are edited in ESS[BUGS] mode. Two keys
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are bound for your use in ESS[BUGS], F2 and F12. F2 performs the same action
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as it does in ESS[SAS], @xref{ESS(SAS)--Function keys for batch processing}.
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F12 performs the function
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ess-bugs-next-action which you will use a lot. Pressing F12 in an empty buffer
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for a model file will produce a template for you.
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ESS[BUGS] supports "replacement" variables. These variables are created as
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part of the template, i.e. with the first press of F12 in an empty buffer.
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all capitals and start with '%': %N, %DATA, %INIT, %MONITOR and %STATS.
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When you are finished editing your model file, pressing F12 will perform the
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necessary replacements and build your command file for you.
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The %DATA variable appears in
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the line 'data in "%DATA";'. On the second press of F12, %DATA will be
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replaced by the model file name except it will have the .dat extension. If
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your data file is named something else, then change %DATA in the template to
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the appropriate file name and no replacement will occur.
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The %INIT variable appears in
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the line 'inits in "%INIT";'. On the second press of F12, %INIT will be
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replaced by the model file name except it will have the .in extension. If
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your model will be generating it's own initial values, place a comment
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character, #, at the beginning of the line. Or, if your
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init file is named something else, then change %INIT in the template to the
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appropriate file name.
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The %N variable appears in the line 'const N = 0;#%N'. Although it is commented,
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it is still active. Notice that later on in the template you have the line
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'for (i in 1:N)'. The BUGS constant N is the number of rows in
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your data file. When you press F12, the data file is read and the number of
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lines are counted (after %DATA is resolved, if necessary). The number of
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lines replace the zero in the 'const N = 0' statement.
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The %MONITOR variable appears on a line by itself. Although it is commented,
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it is still active. This line is a list of variables that you want monitored.
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When you press F12, the appropriate statements are created in
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the command file to monitor the list of variables. If the line is blank, then
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the list is populated with the variables from the 'var' statement.
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The %STATS variable is similar to the %MONITOR variable. It is a list of
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variables for which summary statistics will be calculated. When you press
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F12, the appropriate statements will be generated in your command file.
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Please note that the %DATA and %INIT variables are only replaced on the second
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press of F12, but the actions for %N, %MONITOR and %STATS are performed on
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each press of F12 if you re-visit the model file.
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@comment node-name, next, previous, up
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@node ESS(BUGS)--Command files, ESS(BUGS)--Log files, ESS(BUGS)--Model files, ESS for BUGS
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@section ESS[BUGS]--Command files
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To avoid extension name collision, .bmd is used for BUGS command files. When
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you have finished editing your model file and press F12, a command file is
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created if one does not already exist. However, the command file was
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created, it recognizes two "replacement" variables: %MONITOR and %STATS.
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Two %MONITOR variables appears on lines by themselves. Although they are
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commented, they are still active. Between them appears the necessary
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statements to monitor the list of variables specified in the model file. The
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behavior of the %STATS variable is similar.
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When you are finished editing your command file, pressing F12 again will submit
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your command file as a batch job. Batch scripts are provided for both DOS and
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Unix in the etc sub-directory of the ESS distribution. The DOS script is
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called "BACKBUGS.BAT" and the Unix script is "backbugs". These scripts allow
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you to change the number of bins to use in the Griddy algorithm
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(Metropolis sampling). That is handled by the variable ess-bugs-default-bins
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@comment node-name, next, previous, up
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@node ESS(BUGS)--Log files, , ESS(BUGS)--Command files, ESS for BUGS
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@section ESS[BUGS]--Log files
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To avoid extension name collision, .bog is used for BUGS log files. The BUGS
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batch script provided with ESS creates the .bog file from the .log file when
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the batch process completes. If you need to look at the .log file while
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the batch process is running, it will not appear in ESS[BUGS] mode unless
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you modify the auto-mode-alist variable. If you have done so, then you
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may find F2 useful to refresh the .log if the batch process over-writes or
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doc/help-bugs.texi
