liebke / incanter

Clojure-based, R-like statistical computing and graphics environment for the JVM

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file .gitignore Wed Dec 23 06:01:03 -0800 2009 fix typo [alexott]
file README.textile Fri Jan 01 22:18:10 -0800 2010 Added function, a aware version of map for us... [liebke]
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directory data/ Tue Dec 29 09:55:41 -0800 2009 removed extra whitespace in sample datasets. [David Liebke]
directory docs/ Sat Dec 12 13:02:19 -0800 2009 removed pre-generated api docs, run bin/generat... [liebke]
file epl-v10.html Wed Mar 11 20:10:13 -0700 2009 added Eclipse Public License file [liebke]
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file pom.xml Sat Dec 26 18:51:23 -0800 2009 Reorganizing build structure a bit [liebke]
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README.textile

Incanter

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

Getting started with Incanter

A pre-built version of Incanter that includes all the necessary dependencies can be downloaded here. 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-bundle/target/incanter-exec.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-bundle/target/incanter-exec.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

Documentation

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

Incanter documentation

Related API documentation

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 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-bundle directory

A Swank server can be started with the bin/swank script or by running mvn clojure:swank, from the modules/incanter-bundle 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.