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@ESS{[BUGS]} was originally designed for use with BUGS software.
Later, it evolved to support JAGS as a dialect of the
BUGS language via @ESS{[JAGS]}, however, @ESS{[JAGS]} is documented in
the section Help for JAGS.
@ESS{[BUGS]} provides 5 features. First, BUGS syntax is described to
allow for proper fontification of statements, distributions,
functions, commands and comments in BUGS model files, command files
and log files. Second, @ESS{} creates templates for the command file
from the model file so that a BUGS batch process can be defined by a
single file. Third, @ESS{} provides a BUGS batch script that allows @ESS{}
to set BUGS batch parameters. Fourth, key sequences are defined to
create a command file and submit a BUGS batch process. Lastly,
interactive submission of BUGS commands is also supported.
@comment node-name, next, previous, up
@node ESS(BUGS)--Model files, ESS(BUGS)--Command files, ESS for BUGS, ESS for BUGS
@section ESS[BUGS]--Model files
Model files with the @file{.bug} extension are edited in @ESS{[BUGS]} mode
if @code{(require 'essd-bugs)} was performed or edited in @ESS{[JAGS]} mode
if @code{(require 'essd-jags)}.
Three keys are bound for your use in @ESS{[BUGS]}, @kbd{F2}, @kbd{C-c C-c} and @kbd{=}.
@kbd{F2} performs the same action as it does in @ESS{[SAS]},
@xref{ESS(SAS)--Function keys for batch processing}. @kbd{C-c C-c} performs the
function @code{ess-bugs-next-action} which you will use a lot. Pressing it
in an empty buffer for a model file will produce a template for you. @kbd{=}
inserts the set operator, @code{<-}.
@ESS{[BUGS]} supports "replacement" variables. These variables are
created as part of the template, i.e. with the first press of @kbd{C-c C-c}
in an empty buffer. They are named by all capitals and start
with @code{%}: @code{%N}, @code{%DATA}, @code{%INIT}, @code{%MONITOR} and
@code{%STATS}. When you are
finished editing your model file, pressing @kbd{C-c C-c} will perform
the necessary replacements and build your command file for you.
The @code{%DATA} variable appears in the line @code{data in "%DATA";}. On the
second press of @kbd{C-c C-c}, @code{%DATA} will be replaced by the model file name
except it will have the @file{.dat} extension. If your data file is named
something else, then change @code{%DATA} in the template to the appropriate
file name and no replacement will occur.
The @code{%INIT} variable appears in the line @code{inits in "%INIT";}.
On the second press of @kbd{C-c C-c}, @code{%INIT} will be
replaced by the model file name except it will have the .in extension.
If your model will be generating it's own initial values, place a
comment character, @code{#}, at the beginning of the line. Or, if your init
file is named something else, then change @code{%INIT} in the template to the
appropriate file name.
The @code{%N} variable appears in the line @code{const N = 0;#%N}.
Although it is commented, it is still active. Notice that later on in
the template you have the line @code{for (i in 1:N)}. The BUGS
constant @code{N} is the number of rows in your data file. When you
press @kbd{C-c C-c}, the data file is read and the number of lines are
counted (after @code{%DATA} is resolved, if necessary). The number of
lines replace the zero in the @code{const N = 0;} statement.
The @code{%MONITOR} variable appears on a line by itself. Although it
is commented, it is still active. This line is a list of variables
that you want monitored. When you press @kbd{C-c C-c}, the
appropriate statements are created in the command file to monitor the
list of variables. If the line is blank, then the list is populated
with the variables from the @code{var} statement.
The @code{%STATS} variable is similar to the @code{%MONITOR} variable.
It is a list of variables for which summary statistics will be
calculated. When you press @kbd{C-c C-c}, the appropriate statements
will be generated in your command file.
Please note that the @code{%DATA} and @code{%INIT} variables are only
replaced on the second press of @kbd{C-c C-c}, but the actions for
@code{%N}, @code{%MONITOR} and @code{%STATS} are performed on each
press of @kbd{C-c C-c} if you re-visit the model file.
@comment node-name, next, previous, up
@node ESS(BUGS)--Command files, ESS(BUGS)--Log files, ESS(BUGS)--Model files, ESS for BUGS
@section ESS[BUGS]--Command files
To avoid extension name collision, @file{.bmd} is used for BUGS
command files and @file{.jmd} for JAGS command files. When you have
finished editing your model file and press @kbd{C-c C-c}, a command
file is created if one does not already exist. However, the command
file was created, it recognizes two "replacement" variables:
@code{%MONITOR} and @code{%STATS}.
Two @code{%MONITOR} variables appears on lines by themselves.
Although they are commented, they are still active. Between them
appears the necessary statements to monitor the list of variables
specified in the model file. The behavior of the @code{%STATS}
variable is similar.
When you are finished editing your command file, pressing @kbd{C-c C-c}
again will submit your command file as a batch job. BUGS batch
scripts are provided for both Unix and DOS in the @file{etc}
sub-directory of the @ESS{} distribution. The Unix script is
@file{backbugs} for BUGS major version 0.6 and @file{backbug5} for
0.5. The DOS script is @file{BACKBUGS.BAT} for BUGS major version 0.6
only. These scripts allows @ESS{} access to BUGS batch features that
are not readily available with the batch scripts that come with BUGS.
@comment node-name, next, previous, up
@node ESS(BUGS)--Log files, , ESS(BUGS)--Command files, ESS for BUGS
@section ESS[BUGS]--Log files
To avoid extension name collision, @file{.bog} is used for BUGS log
files. The BUGS batch script provided with @ESS{} creates the
@file{.bog} file from the @file{.log} file when the batch process
completes. If you need to look at the @file{.log} file while the
batch process is running, it will not appear in @ESS{[BUGS]} mode.
You may find @kbd{F2} useful to refresh the @file{.log} if the batch
process over-writes or appends it.
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