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 |