# Describe and Simulate Breeding Schemes

## Documentation for package ‘BreedingSchemeLanguage’ version 0.9.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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