set_siteByState_fitnessMat {rSHAPE}

This function is designed to establish an initial object which maps the fitness values of genome positions based on the state of that site. At present, this has no meaning if the model of simulation is no NK, Additive, or Fixed. Where the first is Kauffman's NK model and form of calculations, Additive is what that word would make you think for fitness effects of mutations at sites, and Fixed is when user supplied a defined fitness matrix that describes the entire fitness landscape. NOTE: This function should likely be called without supplying any non-default arguments as it will use the shape_ options defined.

Description

This function is designed to establish an initial object which maps the fitness values of genome positions based on the state of that site. At present, this has no meaning if the model of simulation is no NK, Additive, or Fixed. Where the first is Kauffman's NK model and form of calculations, Additive is what that word would make you think for fitness effects of mutations at sites, and Fixed is when user supplied a defined fitness matrix that describes the entire fitness landscape. NOTE: This function should likely be called without supplying any non-default arguments as it will use the shape_ options defined.

Usage

set_siteByState_fitnessMat(func_simModel = getOption("shape_simModel"),
  func_const_fixedFrame = getOption("shape_const_fixedFrame"),
  func_const_siteStates = getOption("shape_const_siteStates"))

Arguments

func_simModel

This is the fitness landscape model being simulated

func_const_fixedFrame

This is a contextual object that described constant fitness effects

func_const_siteStates

These are the posibble states for genome sites, at present this ought to be "0" and/or "1"

Value

A contextually meaningful matrix describing fitness effects of mutations/genotypes, where based on the context NULL may be returned.

Note

There is no example as this cannot work outisde of a runSHAPE call, it requires data produced by the simulation experiment.