• 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 R-like semantics (if not always syntax) and interactive-programming environment to the development of stand-alone statistical applications, with web or gui front-ends, as well as to the development of statistical applications that need to plug into an existing software infrastructure in order to consume data, from databases or other information systems, or drive other processes. Clojure’s seamless integration with Java makes this kind of development much simpler than is possible in R, and Incanter’s R-like semantics makes it 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 the Clojure shell (aka the REPL) from the Incanter directory: bin/clj. (Note: bin/clj is a bash script, and won’t run on Windows systems as is.)

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)))

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 in the docs/api/ directory and online at https://incanter.org/docs/api/.

More Incanter examples

• See Incanter wiki
  • Sample plots
  • Matrices
  • Datasets
  • Statistics examples
  • Probability distributions
• See the examples/ directory and tests/test-cases.clj for additional usage examples
  • Run examples/run_prob_plots.clj to generate example probability distribution plots
  • Run tests/runtests.clj to run test cases

Documentation

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

• Incanter Wiki
• Incanter API

• Clojure API
• Parallel Colt Java API
• JFreeChart Java API

Building Incanter

The Incanter distribution includes a pre-built jar file, but if you would like to build it, test it, and generated the api documentation yourself, run the following commands from the Incanter directory:

• Build incanter.jar: ant
• Run unit tests: tests/runtests.clj
• Generate API docs: bin/generate_docs.clj

(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 (test-is, gen-html-docs, repl-utils)
• JLine