HybridPop-class         Hybrid population
LociMap-class           Loci metadata
MapPop-class            Raw population with genetic map
MultiPop-class          Multi-Population
NamedMapPop-class       Raw population with genetic map and id
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           Sex specific additive trait
TraitA2D-class          Sex 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
addSegSite              Add segregating site to MapPop
asCategorical           Convert a normal (Gaussian) trait to an ordered
                        categorical (threshold) trait
attrition               Lose individuals at random
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
getGenMap               Get genetic map
getNumThreads           Number of available threads
getPed                  Get pedigree
getQtlMap               Get QTL genetic map
getSnpMap               Get SNP genetic map
gv                      Genetic value
hybridCross             Hybrid crossing
importGenMap            Import genetic map
importHaplo             Import haplotypes
importInbredGeno        Import inbred, diploid genotypes
isFemale                Test if individuals of a population are female
                        or male
isPop                   Test if object is of a Population class
makeCross               Make designed crosses
makeCross2              Make designed crosses
makeDH                  Generates DH lines
meanEBV                 Mean estimated breeding values
meanG                   Mean genetic values
meanP                   Mean phenotypic values
mendelianSampling       Calculate Mendelian sampling
mergeGenome             Combine genomes of individuals
mergePops               Merge list of populations
mutate                  Add Random Mutations
nInd                    Number of individuals
newEmptyPop             Creates an empty population
newMapPop               New MapPop
newMultiPop             Create new Multi Population
newPop                  Create new population
parentAverage           Calculate parent average
pedigreeCross           Pedigree cross
pheno                   Phenotype
popVar                  Population variance
pullIbdHaplo            Pull IBD haplotypes
pullMarkerGeno          Pull marker genotypes
pullMarkerHaplo         Pull marker haplotypes
pullQtlGeno             Pull QTL genotypes
pullQtlHaplo            Pull QTL haplotypes
pullSegSiteGeno         Pull segregating site genotypes
pullSegSiteHaplo        Pull seg site haplotypes
pullSnpGeno             Pull SNP genotypes
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 estimated breeding values (EBV)
setMarkerHaplo          Set marker haplotypes
setPheno                Set phenotypes
setPhenoGCA             Set GCA as phenotype
setPhenoProgTest        Set progeny test as phenotype
smithHazel              Calculate Smith-Hazel weights
solveMKM                Solve Multikernel Model
solveMVM                Solve Multivariate Model
solveRRBLUP             Solve RR-BLUP
solveRRBLUPMK           Solve Multikernel RR-BLUP
solveRRBLUPMV           Solve Multivariate RR-BLUP
solveRRBLUP_EM          Solve RR-BLUP with EM
solveRRBLUP_EM2         Solve RR-BLUP with EM and 2 random effects
solveRRBLUP_EM3         Solve RR-BLUP with EM and 3 random effects
solveUVM                Solve Univariate Model
usefulness              Usefulness criterion
varA                    Additive variance
varAA                   Additive-by-additive epistatic variance
varD                    Dominance variance
varEBV                  Variance of estimated breeding values
varG                    Total genetic variance
varP                    Phenotypic variance
writePlink              Writes a Pop-class as PLINK files
writeRecords            Write data records
