evaluate.Galgo: Evaluates all chromosomes with a fitness function

In galgo: Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data

Description

Evaluates all chromosomes with a fitness function. The result of this evaluation is treated as the “fitness” value (as defined by Goldberg, see references). The Galgo object call this method and store the returned value asociated with each chromosome in order to decide which chromosomes are the best choices to be part of the next generation. The “fitness function” commonly returns a numeric value scaled from 0 to 1 (but not always, For more information see Galgo.). As close to 1 as better chance it could be part of the next generation.

Usage

## S3 method for class 'Galgo'
evaluate(.O, fn=.O$fitnessFunc, parent=NULL, ...)

Arguments

fn	The “fitness” function to be called to evaluate all chromosomes. It should follow the format function(obj, parent) { ... }. The default is to use the function specified in the Galgo object.
parent	The original object calling for the evaluation. This is passed when the function is sensitive to data stored in parent object. Commonly it is a BigBang object (perhaps Galgo instead).

Value

Returns nothing.

Author(s)

Victor Trevino. Francesco Falciani Group. University of Birmingham, U.K. http://www.bip.bham.ac.uk/bioinf

References

Goldberg, David E. 1989 Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley Pub. Co. ISBN: 0201157675

See Also

For more information see Galgo.

Examples

  cr <- Chromosome(genes=newCollection(Gene(shape1=1, shape2=100),5))
  ni <- Niche(chromosomes = newRandomCollection(cr, 10))
  wo <- World(niches=newRandomCollection(ni,2))

  ga <- Galgo(populations=newRandomCollection(wo,1), goalFitness = 0.75,
              callBackFunc=plot,
              fitnessFunc=function(chr, parent) 5/sd(as.numeric(chr)))
  ga
  summary(ga)
  evaluate(ga) # manual evaluation
  ga$generation <- ga$generation + 1
  ga
  refreshStats(ga)
  ga           # updated values
  summary(ga)  # but chromosomes have not been "evolved"

  evolve(ga) 
  # the usual evaluation of fitness function is inside evolve method

galgo documentation built on May 2, 2019, 4:20 a.m.