BASSIST(1)           Bassist Quick Reference           BASSIST(1)


NAME
       bassist - compiles Bayesian models to simulator programs

SYNOPSIS
       bassist [-d  debugflags] [-hvpEc] [-o prog] [-s[dir] [-f]]
       [-i file] [-I dir] [-L dir] [-l lib] filename...

DESCRIPTION
       Bassist is a set of software for doing Metropolis-Hastings
       sampling on Bayesian models.  bassist is the compiler tool
       which takes a model description and generates a  simulator
       program, which in turn reads in data and produces a sample
       from the joint distribution (in the MCMC sense).

       The model specification is written in a text file  in  the
       Bassist  model  specification  language. The specification
       file is given as input to bassist, which compiles it to an
       executable  simulation  program.  The  simulation  program
       reads the data files and runs the simulation, during which
       the  results  are  written  to  the  standard  output. The
       results may be directed to a file or to  a  data  analysis
       program,  for  example javist, a visualization tool imple­
       mented at University of Helsinki, Department  of  Computer
       Science.

OPTIONS
       -d debugflags
              Turn  on the debug flags listed in debugflags.  The
              debug feature is not usable in this version.

       -h     Print a short help message and exit.

       -v     Turn on detailed  reporting.   Presently  non-func­
              tional.

       -p     Print  the model specification to the standard out­
              put after the parsing phase.

       -E     Validate the model syntax by parsing it,  and  exit
              after the parsing phase.

       -c     Only compile the model into C++, do not compile the
              resulting files into  a  binary.  Not  very  useful
              without -s.

       -o prog
              Give  the generated simulator program the file name
              prog instead of the default modelname.sim.

       -s[dir]
              Copy the simulator source  code  to  the  directory
              dir,  or if dir is not given, to the default direc­
              tory modelname.src.   If  the  directory  does  not
              exist,  it  will be created. No existing files will



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BASSIST(1)           Bassist Quick Reference           BASSIST(1)


              be overwritten unless -f is also given.

       -f     Used in conjunction with -s  to  force  overwriting
              old  files.  Analoguous to the -f option of several
              Unix commands, but note that the -i option is unre­
              lated.

       -i file
              Compile the code file file with the generated simu­
              lator code.  If  some  user-defined  functions  are
              needed  in the model specification, their implemen­
              tations must be found in file.

       -I dir Add the directory dir to the  include  file  search
              path for the compilation of the simulation program.

       -L dir Add the directory dir to the  library  search  path
              for the compilation of the simulation program.

       -l lib Use the library lib when linking the simulator pro­
              gram.

       -C flags
              Include flags in the C compiler flags used for com­
              piling the simulation program.

ENVIRONMENT
       The  following  environment  variables  allow for run-time
       overriding of compile-time defaults. In  normal  use,  you
       don't need to set them.

       BASSIST_LIBRARY
              The  complete  path  name  of  the Bassist library.
              Defaults       to        /home/jks/bassist/lib/lib­
              Bassist0.8.4.a.

       BASSIST_INCLUDE_DIR
              The  directory  where  the  include  files  of  the
              Bassist   library   are   located.   Defaults    to
              /home/jks/bassist/include/bassist/0.8.4.

       BASSIST_TEMPLATE_DIR
              The directory where the Bassist code template files
              are          located.          Defaults          to
              /home/jks/bassist/share/bassist/0.8.4.

FILES
       /home/jks/bassist/lib/libBassist0.8.4.a
              The   Bassistlibrary  that  simulators  are  linked
              against.

       /home/jks/bassist/include/bassist/0.8.4/*.h
              The include files for the Bassist library.




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BASSIST(1)           Bassist Quick Reference           BASSIST(1)


       /home/jks/bassist/share/bassist/0.8.4/*
              The template files that form the  skeleton  of  all
              generated simulators.

SEE ALSO
       bassist_simulator(1),
       http://www.rni.helsinki.fi/cs/bassist/

AUTHORS
       Elja Arjas,  Karri-Pekka  Laakso,  Heikki  Mannila,  Mikko
       Mäkelä,  Marko  Salmenkivi, Jouni Seppänen, Riikka Suramo,
       Hannu Toivonen, and Kari Vasko  have  contributed  to  the
       development  of  Bassist  at the Rolf Nevanlinna Institute
       and the Department of Computer Science,  both  departments
       of the University of Helsinki.










































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