AlphaSimR               AlphaSimR: Breeding Program Simulations
HybridPop-class         Hybrid population
LociMap-class           Loci metadata
MapPop-class            Raw population with genetic map
Pop-class               Population
RRBLUP                  RR-BLUP Model
RRBLUP2                 RR-BLUP Model 2
RRBLUPMemUse            RRBLUP Memory Usage
RRBLUP_D                RR-BLUP Model with Dominance
RRBLUP_D2               RR-BLUP with Dominance Model 2
RRBLUP_GCA              RR-BLUP GCA Model
RRBLUP_GCA2             RR-BLUP GCA Model 2
RRBLUP_SCA              RR-BLUP SCA Model
RRBLUP_SCA2             RR-BLUP SCA Model 2
RRsol-class             RR-BLUP Solution
RawPop-class            Raw Population
SimParam                Simulation parameters
TraitA-class            Additive trait
TraitA2-class           Gender specific additive trait
TraitA2D-class          Gender specific additive and dominance trait
TraitAD-class           Additive and dominance trait
TraitADE-class          Additive, dominance, and epistatic trait
TraitADEG-class         Additive, dominance, epistasis, and GxE trait
TraitADG-class          Additive, dominance and GxE trait
TraitAE-class           Additive and epistatic trait
TraitAEG-class          Additive, epistasis and GxE trait
TraitAG-class           Additive and GxE trait
aa                      Additive-by-additive epistatic deviations
bv                      Breeding value
cChr                    Combine MapPop chromosomes
calcGCA                 Calculate GCA
dd                      Dominance deviations
doubleGenome            Double the ploidy of individuals
ebv                     Estimated breeding value
editGenome              Edit genome
editGenomeTopQtl        Edit genome - the top QTL
fastRRBLUP              Fast RR-BLUP
genParam                Sumarize genetic parameters
genicVarA               Additive genic variance
genicVarAA              Additive-by-additive genic variance
genicVarD               Dominance genic variance
genicVarG               Total genic variance
getQtlMap               Get QTL genetic map
getSnpMap               Get SNP genetic map
gv                      Genetic value
hybridCross             Hybrid crossing
makeCross               Make designed crosses
makeCross2              Make designed crosses
makeDH                  Generates DH lines
meanG                   Mean genetic values
meanP                   Mean phenotypic values
mergeGenome             Combine genomes of individuals
mergePops               Merge list of populations
mutate                  Add Random Mutations
nInd                    Number of individuals
newMapPop               New MapPop
newPop                  Create new Population
pedigreeCross           Pedigree cross
pheno                   Phenotype
popVar                  Population variance
pullIbdHaplo            Pull Identity By Descent (IBD) haplotypes
pullQtlGeno             Pull QTL genotype
pullQtlHaplo            Pull QTL haplotypes
pullSegSiteGeno         Pull seg site genotypes
pullSegSiteHaplo        Pull seg site haplotypes
pullSnpGeno             Pull SNP genotype
pullSnpHaplo            Pull SNP haplotypes
quickHaplo              Quick founder haplotype simulation
randCross               Make random crosses
randCross2              Make random crosses
reduceGenome            Create individuals with reduced ploidy
resetPop                Reset population
runMacs                 Create founder haplotypes using MaCS
runMacs2                Alternative wrapper for MaCS
sampleHaplo             Sample haplotypes from a MapPop
selIndex                Selection index
selInt                  Selection intensity
selectCross             Select and randomly cross
selectFam               Select families
selectInd               Select individuals
selectOP                Select open pollinating plants
selectWithinFam         Select individuals within families
self                    Self individuals
setEBV                  Set EBV
setPheno                Set phenotypes
setPhenoGCA             Set GCA as phenotype
smithHazel              Calculate Smith-Hazel weights
usefulness              Usefulness criterion
varA                    Additive variance
varAA                   Additive-by-additive epistatic variance
varD                    Dominance variance
varG                    Total genetic variance
varP                    Phenotypic variance
writePlink              Writes a Pop-class as PLINK files
writeRecords            Write data records
