liebke / incanter

• Overview
• Getting started with Clojure
• Getting started with Incanter
• Documentation and examples
• Building Incanter
• Dependencies

Overview and motivation

Incanter is a Clojure-based, R-like statistical computing and graphics environment for the JVM. At the core of Incanter are the Parallel Colt numerics library, a multithreaded version of Colt, and the JFreeChart charting library, as well as several other Java and Clojure libraries.

The motivation for creating Incanter is to provide a JVM-based statistical computing and graphics platform with R-like semantics and interactive-programming environment. Running on the JVM provides access to the large number of existing Java libraries for data access, data processing, and presentation. Clojure’s seamless integration with Java makes leveraging these libraries much simpler than is possible in R, and Incanter’s R-like semantics makes statistical programming much simpler than is possible in pure Java.

Motivation for a Lisp-based R-like statistical environment can be found in the paper Back to the Future: Lisp as a Base for a Statistical Computing System by Ihaka and Lang (2008). Incanter is also inspired by the now dormant Lisp-Stat (see the special volume in the Journal of Statistical Software on Lisp-Stat: Past, Present, and Future from 2005).

Motivation for a JVM-based Lisp can be found at the Clojure website, and screencasts of several excellent Clojure talks by the language’s creator, Rich Hickey, can be found at clojure.blip.tv.

Getting started with Clojure

For a great introduction to programming in Clojure, read Clojure – Functional Programming for the JVM. by R. Mark Volkmann. For an even more extensive introduction, get the newly released book Programming Clojure by Stuart Halloway.

Other Clojure resources

• Clojure website
• Clojure Google group
• clojure.blip.tv
• Clojure Programming Wikibook
• Learning Clojure Wikibook

Getting started with Incanter

Start by visiting the Incanter website for an overview, checkout the documentation page for a listing of HOW-TOs and examples, and then download a pre-built version of Incanter, which includes all the necessary dependencies, and unpack the file (if you would like to build it from source, read Building Incanter).

Start the Clojure shell (aka the REPL) from the Incanter directory: bin/clj or bin\clj.bat on Windows (note: if you want to start the Clojure REPL from a directory other than the top level Incanter directory, change the INCANTER_HOME variable in the clj script so that it uses an absolute path instead the ./ directory).

You can also start Incanter directly with the following command:
java -jar modules/incanter-app/target/incanter-app-*.jar
This will start a Clojure REPL, but will not have command history like the clj scripts. If you want to use the built-in data sets, you’ll also need to set the incanter.home property as follows:
java -Dincanter.home=/path/to/incanter/dir -jar modules/incanter-app/target/incanter-app-*.jar

From the Clojure shell, load the Incanter libraries:

(use '(incanter core stats charts))

Try an example: sample 1,000 values from a standard-normal distribution and view a histogram:

(view (histogram (sample-normal 1000)))

Try another simple example, a plot of the sine function over the range -4 to 4:

(view (function-plot sin -4 4))

The online documentation for most Incanter functions contain usage examples. The documentation can be viewed using Clojure’s doc function. For example, to view the documentation and usage examples for the linear-model function, call (doc linear-model) from the Clojure shell. Use (find-doc "search term") to search the online documentation from the Clojure shell. The API documentation can also be found at http://liebke.github.com/incanter.

More Incanter examples

• See the Incanter blog
• See Incanter wiki
  • Sample plots
  • Matrices
  • Datasets
  • Statistics examples
  • Probability distributions
• See the examples/ directory for additional usage examples.
  • bin/clj examples/run_prob_plots.clj to generate example probability distribution plots

Documentation

The following documentation covers the Incanter and Clojure APIs and the APIs of the underlying java libraries.

Incanter documentation

• Doc Index
• API

Related API documentation

• Clojure API
  *"Clojure-contrib API":http://richhickey.github.com/clojure-contrib/
• Parallel Colt Java API
• JFreeChart Java API
  Processing API
  Joda Time API

Building Incanter

To build and test Incanter, you will need to have Maven and git installed:

• First, clone the Incanter Github repository: git clone git://github.com/liebke/incanter.git
• cd into the incanter directory
• use Maven to build, test, and install Incanter: mvn install
• to build Incanter without running tests or installing jars in the Maven repository, run: mvn package -Dmaven.test.skip=true

To start up a Clojure REPL with Incanter and its dependencies in the CLASSPATH, run: bin/clj (or on Windows bin/clj.bat)

or run: mvn clojure:repl , from the modules/incanter-app directory

or run java -jar modules/incanter-app/target/incanter-app-1.0-master-SNAPSHOT.jar

A Swank server can be started with the bin/swank script or by running mvn clojure:swank, from the modules/incanter-app directory, which can be connected to with M-x slime-connect within Emacs.

(Note: the bin/clj and *.clj scripts won’t run on Windows systems as is. Although, the Clojure code contained in the *.clj scripts can be run from the Clojure shell.)

Included dependencies

See lib/license.txt file for license terms of included libraries.

• Clojure
• Parallel Colt
  • Netlib-Java (included with Parallel Colt)
• JFreeChart
  • JCommon (included with JFreeChart)
  • GnuJaxp (included with JFreeChart)
• OpenCSV
• JGraph (for future development)
• Clojure-Contrib
• JLine
• Joda Time