docs.notes.cmd.txt Maven / Gradle / Ivy
The newest version!
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-5.0.0-19.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-5.0.0-19.jar -data munin1.txt -datatype discrete -algorithm
fci -maxDegree 3 -significance 0.5
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-test 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 a tabular data file, if one is using
tabular data as input to the algorithm.
"-covariance" followed by the path to a covariance matrix, if one is using a
covariance matrix for input to the algorithm.
“-datatype” must be followed by either “continuous” or “discrete”. If using
a covariance matrix, this may be omitted, since the data must be continuous.
“-algorithm” must be followed by either “pc”, "cpc", "fci", "cfci", "ccd",
"fges", "bayes_est", "randomDag".
“-maxDegree” is by default -1 (unlimited) but may be followed by any integer >= -1.
This is effective for PC, CPC, FCI, and CFCI, not FGES.
“-significance” is by default 0.05 but may be set to any number in the range
[0.0, 1.0]. This is effective for PC, CPC FCI, and CFCI, not FGES.
"-sampleprior" is by detault 10 but may be set to any positive number; this
is used for FGES.
"-structureprior" is by default 1 but may be set to any positive number; this
is used for FGES.
"-penaltydiscount" is by default 1 but may be set to any positive number; this
is used for FGES.
"- graphxml" followed by a filename will write graphical output to that file
in XML format.
"-graphtxt" followed by a filename will write graphical output to that file
in text format.
"-externalgraphtxt" followed by a file name will read in an initial graph.
This is only used for pairwise algorithms.
"-nodsep" for FCI indicates that the M-Sep search should not be run.
"-rfci" for FCI uses the RFCI variant of the algorithm.
"-rrfci" for FCI uses the RRFCI variant of the algorithm.
"-verbose" if verbose information, e.g. about the independencies tested for
constraint based algorithms, should be output.
"-knowledge" followed by a path to a knowledge file supplied knowledge to
a number of the supported algorithms. The knowledge file should have a form
like the following:
/knowledge
addtemporal
1 X1 X10 X100 X11
2 X14 X13 X12 X16 X15
3 X2 X20 X21 X18 X17 X195
forbiddirect
requiredirect
The above input should generate the following output to standard out:
1. Path to the data file.
2. Verbose output.
3. The final graph.