DH                      DH
addProgenyData          Add progeny information to data after cross,
                        doubledHaploid, or selfFertilize
calcAmatrix             Calculate an additive relationship matrix
calcGenotypicValue      calcGenotypicValue
calcPhenotypicValue     calcPhenotypicValue
cross                   Cross with random mating, or equal
                        contributions, or randomly between two
                        populations
defineCosts             Define the costs that go into breeding Default
                        for some costs is zero because they probably
                        belong to fixed costs
defineSpecies           Define and create species
defineVariances         Define genetic, interaction, and error
                        variances
doubledHaploid          Doubled haploids
genotype                Genotype markers
getCoalescentSim        getCoalescentSim
initializePopulation    Create a founder population
makeDHs                 makeDHs
makeGamete              makeGamete
makeMap                 create map and QTL effects
makeProgenies           makeProgenies
makeProgeny             makeProgeny
makeSelfs               makeSelfs
outputResults           Save the results
pedigreeMate            pedigreeMate
phasedHapMap2mat        Transform a data.frame with a hapmap data in it
                        into a marker dosage and map list
phenotype               Evaluate the phenotypic value
plotData                Plot the results
predGameteMeanVar       predGameteMeanVar
predictValue            Genomic prediction
randomMate              randomMate
randomMateAll           randomMateAll
randomMateNoFam         randomMateNoFam
select                  Select individuals
selfFertilize           Self-fertilize
simHapMap               Generate a data.frame with a hapmap data in it
                        to test phasedHapMap2mat
testParameterOptimality
                        Function to return the optimality of a
                        parameter vector for a breeding scheme given a
                        simulation environment
