AlphaSimR               AlphaSimR: Breeding Program Simulations
GCAsol-class            RR-BLUP GCA Solution
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
RRDsol-class            RR-BLUP Solution with Dominance
RRsol-class             RR-BLUP Solution
RawPop-class            Raw Population
SCAsol-class            RR-BLUP SCA Solution
SimParam                Simulation parameters
SimParam_addSnpChip     Add SNP chip
SimParam_addStructuredSnpChips
                        Add Structured SNP chips
SimParam_addTraitA      Add additive traits
SimParam_addTraitAD     Add additive and dominance traits
SimParam_addTraitADE    Add additive, dominance and epistasis traits
SimParam_addTraitADEG   Add an additive, dominance, and epistasis GxE
                        trait
SimParam_addTraitADG    Add an additive and dominance GxE trait
SimParam_addTraitAE     Add additive and epistasis traits
SimParam_addTraitAEG    Add additive and epistasis GxE traits
SimParam_addTraitAG     Add additive GxE traits
SimParam_manAddSnpChip
                        Manually add SNP chip
SimParam_manAddTrait    Manually add trait
SimParam_new            Create new simulation
SimParam_removeFounderPop
                        Remove founder population
SimParam_removeSnpChip
                        Remove SNP chip
SimParam_removeTrait    Remove trait
SimParam_rescaleTraits
                        Rescale traits
SimParam_resetPed       Reset pedigree
SimParam_restrSegSites
                        Restrict segregating sites
SimParam_setCorE        Set correlated error variance
SimParam_setGender      Set gender in simulation
SimParam_setRecRatio    Set gender specific recombination
SimParam_setTrackPed    Set pedigree tracking
SimParam_setTrackRec    Set recombination tracking
SimParam_setVarE        Set simulation error variance
SimParam_switchFemaleMap
                        Switch female genetic map
SimParam_switchFounderPop
                        Switch founder population
SimParam_switchGenMap   Switch genetic map
SimParam_switchMaleMap
                        Switch male genetic map
SimParam_switchSnpChip
                        Switch SNP chip
SimParam_switchTrait    Switch trait
TraitA-class            Additive 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
calcGCA                 Calculate GCA
dd                      Dominance deviations
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
mergePops               Merge list of populations
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
pullMultipleSnpGeno     Pull SNP genotype for multiple snp chips
pullMultipleSnpHaplo    Pull SNP haplotypes for multiple chips
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
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
