Package index
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`[`(<HybridPop>)c(<HybridPop>)isHybridPop() - Hybrid population
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LociMap-class - Loci metadata
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`[`(<MapPop>)c(<MapPop>)isMapPop() - Raw population with genetic map
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`[`(<MultiPop>)`[[`(<MultiPop>)c(<MultiPop>)length(<MultiPop>)isMultiPop() - Multi-Population
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`[`(<NamedMapPop>)c(<NamedMapPop>)isNamedMapPop() - Raw population with genetic map and id
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`[`(<Pop>)c(<Pop>)show(<Pop>)length(<Pop>) - Population
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RRBLUP() - RR-BLUP Model
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RRBLUP2() - RR-BLUP Model 2
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RRBLUPMemUse() - RRBLUP Memory Usage
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RRBLUP_D() - RR-BLUP Model with Dominance
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RRBLUP_D2() - RR-BLUP with Dominance Model 2
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RRBLUP_GCA() - RR-BLUP GCA Model
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RRBLUP_GCA2() - RR-BLUP GCA Model 2
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RRBLUP_SCA() - RR-BLUP SCA Model
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RRBLUP_SCA2() - RR-BLUP SCA Model 2
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RRsol-class - RR-BLUP Solution
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`[`(<RawPop>)c(<RawPop>)show(<RawPop>)isRawPop() - Raw Population
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SimParam - Simulation parameters
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TraitA-class - Additive trait
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TraitA2-class - Sex specific additive trait
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TraitA2D-class - Sex specific additive and dominance trait
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TraitAD-class - Additive and dominance trait
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TraitADE-class - Additive, dominance, and epistatic trait
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TraitADEG-class - Additive, dominance, epistasis, and GxE trait
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TraitADG-class - Additive, dominance and GxE trait
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TraitAE-class - Additive and epistatic trait
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TraitAEG-class - Additive, epistasis and GxE trait
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TraitAG-class - Additive and GxE trait
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aa() - Additive-by-additive epistatic deviations
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addSegSite() - Add segregating site to MapPop
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attrition() - Lose individuals at random
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bv() - Breeding value
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cChr() - Combine MapPop chromosomes
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calcGCA() - Calculate GCA
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dd() - Dominance deviations
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.newPop() - Create new population (internal)
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doubleGenome() - Double the ploidy of individuals
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ebv() - Estimated breeding value
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editGenome() - Edit genome
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editGenomeTopQtl() - Edit genome - the top QTL
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fastRRBLUP() - Fast RR-BLUP
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genParam() - Sumarize genetic parameters
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genicVarA() - Additive genic variance
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genicVarAA() - Additive-by-additive genic variance
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genicVarD() - Dominance genic variance
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genicVarG() - Total genic variance
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getGenMap() - Get genetic map
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getNumThreads() - Number of available threads
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getPed() - Get pedigree
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getQtlMap() - Get QTL genetic map
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getSnpMap() - Get SNP genetic map
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gv() - Genetic value
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hybridCross() - Hybrid crossing
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importGenMap() - Import genetic map
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importHaplo() - Import haplotypes
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importInbredGeno() - Import inbred, diploid genotypes
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isFemale()isMale() - Test if individuals of a population are female or male
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isPop() - Test if object is of a Population class
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makeCross() - Make designed crosses
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makeCross2() - Make designed crosses
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makeDH() - Generates DH lines
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meanEBV() - Mean estimated breeding values
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meanG() - Mean genetic values
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meanP() - Mean phenotypic values
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mergeGenome() - Combine genomes of individuals
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mergePops() - Merge list of populations
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mutate() - Add Random Mutations
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nInd() - Number of individuals
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newEmptyPop() - Creates an empty population
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newMapPop() - New MapPop
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newMultiPop() - Create new Multi Population
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newPop() - Create new population
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pedigreeCross() - Pedigree cross
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pheno() - Phenotype
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popVar() - Population variance
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pullIbdHaplo() - Pull IBD haplotypes
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pullMarkerGeno() - Pull marker genotypes
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pullMarkerHaplo() - Pull marker haplotypes
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pullQtlGeno() - Pull QTL genotypes
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pullQtlHaplo() - Pull QTL haplotypes
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pullSegSiteGeno() - Pull segregating site genotypes
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pullSegSiteHaplo() - Pull seg site haplotypes
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pullSnpGeno() - Pull SNP genotypes
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pullSnpHaplo() - Pull SNP haplotypes
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quickHaplo() - Quick founder haplotype simulation
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randCross() - Make random crosses
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randCross2() - Make random crosses
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reduceGenome() - Create individuals with reduced ploidy
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resetPop() - Reset population
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runMacs() - Create founder haplotypes using MaCS
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runMacs2() - Alternative wrapper for MaCS
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sampleHaplo() - Sample haplotypes from a MapPop
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selIndex() - Selection index
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selInt() - Selection intensity
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selectCross() - Select and randomly cross
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selectFam() - Select families
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selectInd() - Select individuals
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selectOP() - Select open pollinating plants
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selectWithinFam() - Select individuals within families
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self() - Self individuals
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setEBV() - Set estimated breeding values (EBV)
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setMarkerHaplo() - Set marker haplotypes
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setPheno() - Set phenotypes
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setPhenoGCA() - Set GCA as phenotype
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setPhenoProgTest() - Set progeny test as phenotype
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smithHazel() - Calculate Smith-Hazel weights
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solveMKM() - Solve Multikernel Model
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solveMVM() - Solve Multivariate Model
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solveRRBLUP() - Solve RR-BLUP
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solveRRBLUPMK() - Solve Multikernel RR-BLUP
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solveRRBLUPMV() - Solve Multivariate RR-BLUP
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solveRRBLUP_EM() - Solve RR-BLUP with EM
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solveRRBLUP_EM2() - Solve RR-BLUP with EM and 2 random effects
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solveRRBLUP_EM3() - Solve RR-BLUP with EM and 3 random effects
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solveUVM() - Solve Univariate Model
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transMat() - Linear transformation matrix
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usefulness() - Usefulness criterion
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varA() - Additive variance
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varAA() - Additive-by-additive epistatic variance
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varD() - Dominance variance
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varEBV() - Variance of estimated breeding values
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varG() - Total genetic variance
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varP() - Phenotypic variance
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writePlink() - Writes a Pop-class as PLINK files
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writeRecords() - Write data records