Installation Guide

Welcome to the installation guide for ETIA, a comprehensive automated causal discovery library. Follow the steps below to install the library and its dependencies.

Prerequisites

Before installing ETIA, ensure that you have the following dependencies:

  • Python 3.8+

  • Java 17 (required for Tetrad algorithms in the Causal Learning module)

  • R 4++ (required for some feature selection algorithms in the AFS module)

  • Cytoscape (required for the visualization)

  • MxM package in R (required for AFS, more information on that follows)

  • daggity package in R (required for CRV.adjustment_set, more information on that follows)

You can download and install these dependencies from their official websites:

ETIA Installation

### Installing via PyPi (Upcoming)

Once ETIA is available on PyPi, you will be able to install it directly using pip:

pip install etia

### Installing from Source

To install ETIA from the source code, follow the steps below:

  1. Clone the repository:

git clone <repository-url>
cd etia

  1. Install the required dependencies:

pip install -r requirements.txt

  1. Compile the necessary components:

make all

Java and R Configuration

For using Tetrad algorithms and certain feature selection algorithms, ensure that Java and R are correctly installed.

### Setting up Java:

  1. Install Java 17 from the [official website](https://www.oracle.com/java/technologies/javase-jdk17-downloads.html).

  2. Ensure that the JAVA_HOME environment variable is set:

export JAVA_HOME=/path/to/java

### Setting up R:

  1. Install R 4.4+ from the [official website](https://www.r-project.org/).

  2. Make sure that R is in your system’s PATH:

R --version

3. Install MxM package (this part may take a while), and the daggity package. MxM package is necessary for AFS while daggity is only used in CRV to find the adjustment sets. Note: Depending on the OS you may need to install CMake and GSL (GNU Scientific Library)

Rscipt --vanilla "install.packages("https://cran.r-project.org/src/contrib/Archive/MXM/MXM_1.5.5.tar.gz", type="source", repos=NULL)"
Rscipt --vanilla "install.packages("daggity", repos = "http://cran.us.r-project.org")"

Verify Installation

After installing the library, you can verify the installation by importing the ETIA modules:

import ETIA.AFS as AFS

afs = AFS()

If no errors occur, the installation was successful.

Test the Library

Download test folder from (https://github.com/mensxmachina/ETIA/tree/main/tests) and run .. code-block:: bash

pytest tests/

Next Steps

Once you have installed ETIA, you can proceed to explore its functionalities. Check out the Example Usage section to learn how to use the library effectively.