#---------------------------------------------------------------------------
#
# NKlandscape.py:
#
# a simple implementation of Kauffman's NK model of rugged fitness landscapes
#
# by Lidia Yamamoto, Kraainem, Belgium, November 2013
#
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# Copyright (C) 2015 Lidia A. R. Yamamoto
# Contact: http://www.artificial-chemistries.org/
#
# This file is part of PyCellChemistry.
#
# PyCellChemistry is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# version 3, as published by the Free Software Foundation.
#
# PyCellChemistry is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with PyCellChemistry, see file COPYING. If not, see
# http://www.gnu.org/licenses/
#

Modules
		artchem.BinaryStrings numpy sys

Classes
		NKlandscape class NKlandscape Methods defined here: __init__(self, n, k) create an NK landscape with given n and k, where: n is the total number of genes, and k is the number of epistatic interactions per gene dist2neighbors(self, genome) fitness distance between a given genome and all its 1-mutant neighbors fitness(self, genome) compute the fitness value for the given genome: the average of the individual fitness values of each gene in the genome gene_fitness(self, pos, genome) returns the fitness of the gene at position 'pos' in the given genome; CAUTION!! uses random epistatic matrix, not scalable!!! gene_fitness_ALT(self, pos, genome) returns the fitness of the gene at position 'pos' in the given genome, using alternative pre-built fitness matrix and smaller matrix of epistatic interactions, different from the original method by Kauffman; (doesn't work very well, disabled by default) mk_epistatic(self) build matrix of epistatic interactions: influence of K other genes on the fitness of each of the N genes epi[i,j] = fitness of gene i when the state of K+1 genes (gene i itself plus the K other genes that interact with it) is j CAUTION!! needs big matrix of size N * 2^(K+1), not scalable!! mk_epistatic_ALT(self) alternative way to build a matrix of epistatic interactions: epi[i,j,v] = amount of influence of gene i on gene j when the value of gene i is v (this leads to a smaller matrix, but doesn't work very well, disabled by default) mk_fitness_ALT(self) make a fitness matrix in order to reduce computation load (goes with the mk_epistatic_ALT attempt, doesn't work very well, disabled by default)

Functions
		sweepNKdistance(n) run the NK model for given N and varying K

Generated automatically by pydoc, July 10, 2015

Generated automatically by pydoc, July 10, 2015