Genome-class            'Genome' class
IDgenomeGeneration      Genome identifier
IDgenotypeGeneration    Genotype identifier
IDhaplotypeGeneration   Haplotype identifier
METAPOP_SIMULATION      Simulation of a metapopulation
Metapopulation-class    Metapopulation
MutationMatrix-class    Mutation matrix
Population-class        Population
Selection-class         'Selection' class
alleleFreqMatGeneration
                        Generation of the matrix for calculating
                        allelic frequencies
areThereHomoz           Are there any allelic combinations including
                        homozygosity
catn                    Concatenate, print and line break
check.genome            The validity check for the 'Genome' class
check.metapopulation    The validity check for the 'Metapopulation'
                        class
check.mutationMatrix    The validity check associated with the
                        'MutationMatrix' class
check.population        The validity check for the 'Population' class
check.selection         The validity check for the 'Selection' class
extractAlleleComb       Extract the allele combination
genotyping              Genotyping
getCustomOutput         Getting the custom output
getRecords              Getting the simulation results
getResults              Getting the simulation results
haploCrossMatrix        Haplotype crossing matrix generation
haplotyping             Haplotyping
initialize,Genome-method
                        Initialize method for the 'Genome' class
initialize,Metapopulation-method
                        Initialize method for the 'Metapopulation'
                        class
initialize,MutationMatrix-method
                        Initialize method for the 'MutationMatrix'
                        class
initialize,Population-method
                        Initialize method for the 'Population' class
initialize,Selection-method
                        Initialize method for the 'Selection' class
is.correct.transition.matrix
                        Test if a matrix is a correct transition matrix
is.default.matrix       Test if a matrix is a default matrix
is.probability.matrix   Test if a matrix is of probability
isAffected              Is this haplo/geno-type affected ?
isHaploSelectFormula    Are there any allelic combinations including
                        homozygosity
listing                 Listing for display
meiosisMatrix           Meiosis matrix generation
mutMatFriendly          Individual mutation definition to allelic
                        mutation matrices
mutMatRates             Mutation matrix from rates
mutation                Definition of a mutation
outFunct                Custom output function
print,Genome-method     Print method for the 'Genome' class
print,Metapopulation-method
                        Print method for the 'Metapopulation' class
print,MutationMatrix-method
                        Print method for the 'MutationMatrix' class
print,Population-method
                        Print method for the 'Population' class
print,Selection-method
                        Print method for the 'Selection' class
recombinationMatrix     Recombination matrix generation
rowResultGen            Processing a result (or record) list
selectFormIntoVect      Conversion of selection formulas
selectInputTreatment    Treatment of selection formulas
selection.form.treatment
                        Treatment of a selection formula
setGenome               Setting the genome
setMetapopulation       Setting a metapopulation
setMutationMatrix       Setting the mutation matrix
setPopulation           Setting a population
setSelectNeutral        Setting the selection
setSelectOnGametes      Setting the selection on gametes
setSelectOnGametesProd
                        Setting the selection on gamete production
setSelectOnInds         Setting the selection on individuals
show,Genome-method      Show method for the 'Genome' class
show,Metapopulation-method
                        Show method for the 'Metapopulation' class
show,MutationMatrix-method
                        Show method for the 'MutationMatrix' class
show,Population-method
                        Show method for the 'Population' class
show,Selection-method   Show method for the 'Selection' class
simulate,Metapopulation-method
                        Simulate method for the 'Metapopulation' class
whichHomoz              Which alleles are homozygous in the input?
