MGSurvE.optimization

GA Operators to calculate fitness and perform operations to search through optimization space.

Functions

calcDiscreteFitness(chromosome, landscape[, ...])	Calculates the fitness function of the landscape given a chromosome (in place, so not thread-safe).
calcDiscreteFitnessPseudoInverse(chromosome, ...)	Calculates the fitness function of the landscape given a chromosome (in place, so not thread-safe).
calcDiscreteSexFitness(chromosome[, ...])	Calculates the fitness function of a Male/Female set of landscapes with a weighted sum of the time-to catch between them.
calcFitness(chromosome[, landscape, ...])	Calculates the fitness function of the landscape given a chromosome (in place, so not thread-safe).
calcFitnessPseudoInverse(chromosome[, ...])	Calculates the fitness function of the landscape given a chromosome using the matrix pseudo-inverse function (in place, so not thread-safe).
calcSexFitness(chromosome[, landscapeMale, ...])	Calculates the fitness function of a Male/Female set of landscapes with a weighted sum of the time-to catch between them.
chromosomeIDtoXY(chromosome, ptsID, pointCoords)	Converts a sites-ID crhomosome into a set of XY or lon-lat coordinates.
cxBlend(ind1, ind2, fixedTrapsMask[, alpha])	Mates two chromosomes by "blend" based on the provided mask (in place).
cxDiscreteUniform(ind1, ind2, fixedTraps[, ...])	Mates two chromosomes in place by swapping alleles between them.
exportLog(logbook, outPath, filename)	Dumps a dataframe with the report of the GA's history.
genFixedTrapsMask(trapsFixed[, dims])	Creates a mask for the fixed traps (non-movable).
getCanonicalElements(tau, sitesN, trapsN)	Helper function to return canonical elements of the traps matrix (Q (tau), R (v), I).
getDaysTillTrapped(landscape[, fitFuns])	Gets the number of timesteps until a walker falls into a trap.
getDaysTillTrappedPseudoInverse(landscape[, ...])	Gets the number of timesteps until a walker falls into a trap (using pseudo-inverse matrix function).
getDaysTillTrappedVector(landscape[, fitFuns])	Gets the number of timesteps until a walker falls into a trap in vector form.
getFundamentalFitness(fundamentalMatrix[, ...])	Get fitness from Markov's fundamental matrix.
getFundamentalMatrix(tau, sitesN, trapsN)	Get Markov's fundamental matrix (pseudo-inverse).
getFundamentalMatrixPseudoInverse(tau, ...)	Get Markov's fundamental matrix (inverse).
getFundamentalVector(tau, sitesN)	Get Markov's fundamental vector.
getMarkovAbsorbing(tauCan, trapsN)	Get Markov's absorbing states (deprecated).
getMeanTimeToCapture(canonElems[, ...])	Calculates the average time to capture given the Q, R, I Markov canonical elements.
getTimeToCapture(landscape[, fitFuns, ...])	Wrapper function for 'getMeanTimeToCapture' given a landscape.
importLog(inPath, filename)	Gets the number of timesteps until a walker falls into a trap.
initChromosome(trapsCoords, fixedTrapsMask, ...)	Generates a random uniform chromosome for GA optimization.
initChromosomeMixed(trapsCoords, ...[, indpb])	Generates a compound chromosome for optimization with a coordinates-type composition (currently unusued).
initDiscreteChromosome(ptsIds, fixedTraps[, ...])	Generates a random uniform chromosome for discrete GA optimizations (from available sites).
mutShuffleIndexes(individual, typeOptimMask)	Shuffles allele indices in pairs.
mutateChromosome(chromosome, fixedTrapsMask)	Mutates a chromosome with a probability distribution based on the mutation mask (in place).
mutateChromosomeAsymmetric(chromosome, ...)	Mutates a chromosome with a probability distribution based on the mutation mask with different probabilities for XY elements (in place).
mutateChromosomeMixed(chromosome, ...[, ...])	Generates a compound chromosome for optimization with a coordinates-type composition (currently unusued).
mutateDiscreteChromosome(chromosome, ptsIds, ...)	Mutates a discrete chromosome from the available sites in the landscape (in place).
optimizeDiscreteTrapsGA(landscape[, ...])	Optimizes the traps' positions using a simple GA algorithm.
optimizeTrapsGA(landscape[, generations, ...])	Optimizes the traps' positions using a simple GA algorithm.
optimizeTwoSexesTrapsGA(landscapeMale, ...)	Optimizes the traps' positions using a simple GA algorithm for two-sexes kernels.
reshapeInCanonicalForm(tau, sitesN, trapsN)	Reshapes a migration matrix into canonical form (deprecated).