Describe and Simulate Breeding Schemes


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Documentation for package ‘BreedingSchemeLanguage’ version 0.9.6

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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
DH DH
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