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# Tetrad

The Tetrad project makes algorithms available in Java for causal search and related tasks. Here is the [Dietrich College Carnegie Mellon University web page for Tetrad](https://www.cmu.edu/dietrich/news/news-stories/2020/august/tetrad-sail.html).
Here is the [Simon Initiative page for Tetrad](https://www.cmu.edu/simon/open-simon/toolkit/tools/learning-tools/tetrad.html).

Here is our [project web page](https://sites.google.com/view/tetradcausal) here with current links for artifacts, a list of contributors, and a bit of history.

Here is the web page for the [Center for Causal Discovery](https://www.ccd.pitt.edu/), which also supports the latest version of Tetrad and Causal Command.

## Setting up Java

You will need to have Java on your machine. If you don't already have Java, or would like to update you Java to a more recent version, see our Wiki
article, [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Java-for-Tetrad).

For version 7.5.0, we will support separate builds for JDK 1.8 and JDK 17 (which will generally work for > 1.8). We have realized that there are a number of users who are unable to update from JDK 1.8. We are able to support these users, at least up through version 7.5.0, and perhaps into the future.

## Tetrad GUI Application

This application breaks analysis of causal problems down into modular pieces that can be connected together following the way in which the problems should ideally be analyzed. We have found this to be useful as an educational tool, though it can also be used for causal analysis for those who don't want to analyze data or do simulations using a command-line interface.

To use this, first determine which version of Java you are using by typing in a terminal window,

```
java -version
```

Note that all Tetrad artifacts are downloadable from [Maven Central](https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/).
We have included artifacts compiled under JDK 1.8 and JDK 17, respectively. The Tetrad codebase uses language level 8 and so can be compiled under any version of Java from 1.8 up, but there are incompatibilities between version 1.8 and version > 1.8.

If your version of Java is 1.8 (version 8), please download Java using this link:

[https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.5.0/tetrad-gui-7.5.0-jdk1.8-launch.jar.](https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.5.0-jdk1.8/tetrad-gui-7.5.0-jdk1.8-launch.jar)

If your version of the Java JDK is version 9 or higher, please download the Java launch jar using this link:

[https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.5.0/tetrad-gui-7.5.0-launch.jar.](https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.5.0/tetrad-gui-7.5.0-launch.jar)

This version is compiled under JDK version 17. If other compilations are needed, these can be generated by the user.

You may be able to launch this jar by double clicking the jar file name, though on a Mac, this presents some [security challenges](https://github.com/cmu-phil/tetrad/wiki/Dealing-with-Tetrad-on-a-Mac:--Security-Issues). In any case, on all platforms, the jar may be launched at the command line (with a specification of the amount of RAM you will allow it to use) using this command:

```
java -Xmx[g]G -jar *-launch.jar
```

where [g] is the maximum number of Gigabytes you wish to allocate to the process.

## Command Line

We have a tool, [Causal Command](https://github.com/bd2kccd/causal-cmd), that lets you run Tetrad algorithms at the command line. For Causal Command, we will assume you are using a version of Java greater than 1.8. Please give feedback if this is not adequate for your purposes.

## Python and R Integration

For Python integration, please see the [py-tetrad Python project](https://github.com/cmu-phil/py-tetrad), which shows how to integrate arbitrary Java code in the Tetrad project into a Python workflow using the [JPype Python project](https://jpype.readthedocs.io/en/latest/). The py-tetrad project will by default assume you are using a version of Java greater than 1.8, though it can easily be adjusted ot use version Java 1.8; for help with this, please give feedback.

Also, please see the [causal-learn Python package](https://causal-learn.readthedocs.io/en/latest/), translating some Tetrad algorithms into Python and adding some algorithms not in Tetrad, now part of the [py-why space](https://github.com/py-why)

For R integration, please see the [rpy-tetrad project](https://github.com/cmu-phil/py-tetrad/blob/main/pytetrad/R/), which gives R support through py-tetrad.

## Documentation

If you're new to Tetrad, here is a [Tutorial](https://rawgit.com/cmu-phil/tetrad/development/tetrad-gui/src/main/resources/resources/javahelp/manual/tetrad_tutorial.html). Also, here is
our [Manual](https://htmlpreview.github.io/?https:///github.com/cmu-phil/tetrad/blob/development/docs/manual/index.html). If you like to watch thought-provoking lectures, here are some [lectures on the Center for Causal Discovery site](https://www.ccd.pitt.edu/video-tutorials/).

In addition, here are our [Javadocs](https://www.phil.cmu.edu/tetrad-javadocs/7.5.0).
Here is our [project web page](https://sites.google.com/view/tetradcausal) with current links for downloadables, a list of contributors, some history, and links to our various projects.

## Install

Expand All @@ -76,25 +14,8 @@ The project contains well-developed code in these packages:

The tetrad-lib package contains the model code; the tetrad-gui package contains the view (GUI) code.

## Feedback

Please submit feedback using our [GitHub Issue Tracker](https://github.com/cmu-phil/tetrad/issues). We will try to the extent possible to resolve all reported issues before [releasing new versions of Tetrad](https://github.com/cmu-phil/tetrad/releases). This may involve moving items to our [Wish List](https://github.com/cmu-phil/tetrad/wiki/Current-Wish-List).

## Open Code

All of our code is public and we welcome suggestions, especially suggestions that improve clarity or performance of our code, or suggestions that press us in new, helpful, directions.

If you're writing code using (or for!) Tetrad in either [Java](https://github.com/cmu-phil/tetrad) or [Python](https://github.com/cmu-phil/py-tetrad) (or R, which we're working toward!), thank you! Please contribute your amazing work, or publish and send us links to your papers. Please keep us abreast of how Tetrad could be improved for your applications; we will do what we can.

## Citation

Please cite as:

```
@inproceedings{ramsey2018tetrad,
title={TETRAD—A toolbox for causal discovery},
author={Ramsey, Joseph D and Zhang, Kun and Glymour, Madelyn and Romero, Ruben Sanchez and Huang, Biwei and Ebert-Uphoff, Imme and Samarasinghe, Savini and Barnes, Elizabeth A and Glymour, Clark},
booktitle={8th international workshop on climate informatics},
year={2018}
}
```