register_GA

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Register a Genetic Algorithm Seriation Method

Register a GA-based seriation metaheuristic.

Keywords
cluster, optimize
Usage
register_GA()
Details

Registers the method "GA" for seriate. This method can be used to optimize any criterion in package seriation. control for seriate with method "GA" accepts the following parameters:

"criterion"
criterion to optimize. Default: BAR
"suggestions"
suggestions to warm start the GA. NA means no warm start. Default: TSP, QAP_LS and Spectral.
"selection"
Selection operator (see GA). Default: non-linear rank selection
"crossover"
Crossover operator (see GA). Default: ordered crossover (OX)
"mutation"
Mutation operator (see GA). Default: a mixture of the simple insertion (80% chance) and simple inversion (20% chance) operators.
"pmutation"
proability for permutations. Default: .5
"pcrossover"
probability for crossover. Default: .2
"popsize"
the population size. Default: 100
"maxiter"
maximum number of generations. Default: 1000
"run"
stop after run generations without improvement. Default: 50
"parallel"
use multiple cores? Default: TRUE
"verbose"
Report progress? Default: TRUE

The GA uses by default the ordered cross-over (OX) operator. For mutation, the GA uses a mixture of simple insertion and simple inversion operators. This mixed operator is created using seriation::gaperm_mixedMutation(ismProb = .8), where ismProb is the probability that the simple insertion mutation operator is used. See package GA for a description of other available cross-over and mutation operators for permutaitons. The appropriate operator functions in GA start with gaperm_.

We warm start the GA using "suggestions" given by several heuristics. Set "suggestions" to NA to start with a purely random initial population.

Note: Package GA needs to be installed.

References

Luca Scrucca (2013): GA: A Package for Genetic Algorithms in R. Journal of Statistical Software, 53(4), 1--37. URL http://www.jstatsoft.org/v53/i04/.

See Also

seriate, ga in GA.

Aliases
  • register_GA
  • GA
  • ga
  • gaperm_mixedMutation
Examples
## Not run: ------------------------------------
# register_GA()
# list_seriation_methods("dist")
# 
# d <- dist(random.robinson(50, pre=TRUE, noise=.1))
# 
# ## use default settings: Banded AR form
# o <- seriate(d, "GA")
# pimage(d, o)
# 
# ## optimize for linear sertiation criterion (LS)
# o <- seriate(d, "GA", control = list(criterion = "LS"))
# pimage(d, o)
# 
# ## no warm start
# o <- seriate(d, "GA", control = list(criterion = "LS", suggestions = NA))
# pimage(d, o)
## ---------------------------------------------
Documentation reproduced from package seriation, version 1.2-2, License: GPL-3

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