BISON BIOGEME run

Invoking Biogeme

Biogeme is invoked in a shell under Linux, in a DOS command window or a Cygwin command window under Windows using the following statement structure

biogeme model_name sample_file_1 sample_file2 sample_file3 ...

By default, the sample_file_1 is assumed to be sample.dat, and the model_name to be default. Therefore, typing

biogeme model_name

is equivalent to typing

biogeme model_name sample.dat

and typing

biogeme

is equivalent to typing

biogeme default sample.dat

Finally, typing

biogeme -h

generates an output looking like

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BIOGEME Version n.x [date]
Michel Bierlaire, EPFL
-- Compiled by Michel Bierlaire on MINGW32_NT-5.1
See http://biogeme.epfl.ch
                    !! CFSQP is available !!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        "In every non-trivial program there is at least one bug."

Usage: biogeme model_name sampleFile1 sampleFile2 sampleFile3 ... 

If the name of the model is mymodel, say, Biogeme reads the following files:

  • a file containing the parameters controlling the behavior of Biogeme: mymodel.par,
  • a file containing the model specification: mymodel.mod,
  • a file containing the data: sample.dat,
  • optionally a file containing the random numbers to use if estimation is based on simulation.

It automatically generates the following output files:

  • a file reporting the results of the estimation: mymodel.rep,
  • the same file in HTML format: mymodel.html,
  • a file containing the main results in LaTeX format: mymodel.tex,
  • a file containing the main results in ALogit format: mymodel.F12,
  • a file containing the specification of the estimated model, in the same format as the model specification file: mymodel.res,
  • a file containing the specification of the estimated model at each iteration, in the same format as the model specification file: mymodel.bck (only if the parameter gevSaveIntermediateResults is set to one),
  • a file containing some descriptive statistics on the data: mymodel.sta,
and the following files to help understanding possible problems
  • a file containing messages produced by Biogeme during the run: mymodel.log,
  • a file containing the values of the parameters which have been actually used by Biogeme: parameters.out,
  • a file containing the data stored in Biogeme to represent the model: model.debug,
  • a file containing the specification of the model, as it has actually been understood by Biogeme: __specFile.debug.
These file names may be modified, according to the following rules:
  1. If an input file mymodel.xxx does not exist, Biogeme attempts to open the file default.xxx. If this file does not exist, Biogeme exits with an error. Typically, the parameter file is not model-dependent. Therefore, it is common to call it default.par to avoid copying it for each different model to be estimated.
  2. If an output file mymodel.xxx already exists, Biogeme does not overwrite it. Instead, it creates the file mymodel~1.xxx. If the file mymodel~1.xxx exists, Biogeme creates the file mymodel~2.xxx, and so on.
To avoid any ambiguity, Biogeme displays the filenames it has actually used for a specific run, for instance
BIOGEME Input files
===================
Parameters:                     default.par
Model specification:            mymodel.mod
Sample 1 :                      sample.dat
Sample 2 :                      sample2.dat
BIOGEME Output files
====================
Estimation results:             mymodel~3.rep
Estimation results (HTML):      mymodel~3.html
Estimation results (Latex):     mymodel~5.tex
Estimation results (ALogit):    mymodel~1.F12
Result model spec. file:        mymodel~2.res
Sample statistics:              mymodel~1.sta
BIOGEME Debug files
===================
Log file:                       mymodel.log
Parameters debug:               parameters.out
Model debug:                    model.debug
Model spec. file debug:         __specFile.debug
Biogeme also generates a file called summary.html where a summary of all runs performed in the working directory are gathered. The name of this file can be modified. It is highly recommended to regularly clean the working directory and save the output files in a different place.
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