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.
Author(s)
Michael Hahsler
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.
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)
## End(Not run)