dummy-link

NKLandscapes

A Julia library for working with the NK family of fitness landscapes.

Readme

Build Status codecov.io NKLandscapes NKLandscapes

NKLandscapes.jl

A Julia library for conducting evolutionary experiments using the NK family of fitness landscapes.

Authors

About NK Landscapes

From Wikipedia:

The NK model is a mathematical model described by its primary inventor
Stuart Kauffman as a "tunably rugged" fitness landscape. "Tunable
ruggedness" captures the intuition that both the overall size of the
landscape and the number of its local "hills and valleys" can be adjusted
via changes to its two parameters, N and K...

The NK landscape model, and its various derivatives, are particularly useful for studying the process of evolution, both biological and computational, because they can be constructed to exhibit a variety of interesting properties including neutrality..

Install

NKLandscapes is listed in the Julia package index, so installation of the most recent release is as simple as Pkg.add("NKLandscapes").

The library is still under heavy development, and it has not (yet) been fully documented. We are making good progress, however, so many functions available already have documentation available when running in the Julia REPL.

Tests

If the package has been installed using Julia's package management tools, the tests can be run simply by issuing Pkg.test("NKLandscapes") in the Julia REPL.

Tests can be run with the included script. There are (or will be) several test suites. First, a set of unit tests that exercise basic functionality and check for sane results. For the most part, these may be thought of as regression tests. Second, there are functional tests that replicate experiments drawn from the literature and check that the results approximately match the published results.

The unit tests may be run with ./runtests.sh unit. The functional tests may be run with ./runtests.sh SUITE where SUITE is one of the following:

  • kauffman - experiments from [1]
  • nowak - experiments from [2]

Note that these tests may take quite a long time to finish even on a very powerful workstation.

Bibliography

  1. Kauffman, S. A. (1993). The Origins of Order: Self-Organization and Selection in Evolution. New York, New York, USA: Oxford University Press.
  2. Nowak, S., & Krug, J. (2015). Analysis of adaptive walks on NK fitness landscapes with different interaction schemes. Journal of Statistical Mechanics: Theory and Experiment, 2015(6), P06014.

TODO

  • Implement all four Nowak and Krug random walk strategies.
  • Finish functional tests.
  • Store fitnesses with population to avoid recomputing them.
  • Add tests for bit string enumeration code.

First Commit

08/11/2015

Last Touched

about 2 years ago

Commits

164 commits

Used By: