Command Line Tetrad.

Step 1: Find the command line jar online. (The version number listed is old;
you will need to substitute the version number you're using.)

http://www.phil.cmu.edu/projects/tetrad_download/download/tetradcmd-4.3.3-1.jar

Step 2: Put this jar in the directory you intend to work in, together with the data file
(which I assume here to be munin1.txt).

Step 3: Type this command:

java -jar tetradcmd-4.3.3-1.jar -data munin1.txt -datatype discrete -algorithm
fci -depth 3 -significance 0.5 -level finer

I'm assuming that tetradcmd.jar and munin1.txt are in the same directory you're
typing in. I'm assuming you're on a Unix-type machine and have JDK 1.4.2 or
higher installed. I'm assuming munin1.txt is the data file that was sent to me
earlier with 189 variables and 5000 cases. I'm assuming that the delimiter for
the data file is whitespace, or regex " *[\t ] *".

The flags “-data”, “-datatype”, and “-algorithm” are required.

“-data” must be followed by the path to the data file.

“-datatype” must be followed by either “continuous” or “discrete”.

“-algorithm” must be followed by either “pc”, "cpc", "fci", "cfci", "ccd",
"ges", "bayes_est", "randomDag".

“-depth” is by default -1 (unlimited) but may be followed by any integer >= -1.

“-significance” is by default 0.05 but may be set to any number in the range
[0.0, 1.0].

"-samplePrior" is by detault 10 but may be set to any positive number; this
is used for GES.

"-structurePrior" is by default 1 but may be set to any positive number; this
is used for GES.

"-discountpenalty" is by default 1 but may be set to any positive number; this
is used for GES.

The above input should generate the following output to standard out:

1. A message that data is being loaded, path to file, data type.

2. When data is loaded, a message indicating # variables and # cases.

3. All of the logged output for the algorithm of choice at the logging level
specified.

4. The final graph.