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A B C D E F G H L M N P Q R S T U V W misc
| AlphaSimR-package | AlphaSimR: Breeding Program Simulations |
| aa | Additive-by-additive epistatic deviations |
| AlphaSimR | AlphaSimR: Breeding Program Simulations |
| bv | Breeding value |
| c-method | Hybrid population |
| c-method | Raw population with genetic map |
| c-method | Population |
| c-method | Raw Population |
| calcGCA | Calculate GCA |
| dd | Dominance deviations |
| ebv | Estimated breeding value |
| editGenome | Edit genome |
| editGenomeTopQtl | Edit genome - the top QTL |
| fastRRBLUP | Fast RR-BLUP |
| GCAsol-class | RR-BLUP GCA Solution |
| genicVarA | Additive genic variance |
| genicVarAA | Additive-by-additive genic variance |
| genicVarD | Dominance genic variance |
| genicVarG | Total genic variance |
| genParam | Sumarize genetic parameters |
| getQtlMap | Get QTL genetic map |
| getSnpMap | Get SNP genetic map |
| gv | Genetic value |
| hybridCross | Hybrid crossing |
| HybridPop-class | Hybrid population |
| LociMap-class | Loci metadata |
| makeCross | Make designed crosses |
| makeCross2 | Make designed crosses |
| makeDH | Generates DH lines |
| MapPop-class | Raw population with genetic map |
| meanG | Mean genetic values |
| meanP | Mean phenotypic values |
| mergePops | Merge list of populations |
| newMapPop | New MapPop |
| newPop | Create new Population |
| nInd | Number of individuals |
| pedigreeCross | Pedigree cross |
| pheno | Phenotype |
| Pop-class | Population |
| 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 |
| RawPop-class | Raw Population |
| resetPop | Reset 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 |
| runMacs | Create founder haplotypes using MaCS |
| runMacs2 | Alternative wrapper for MaCS |
| sampleHaplo | Sample haplotypes from a MapPop |
| SCAsol-class | RR-BLUP SCA Solution |
| selectCross | Select and randomly cross |
| selectFam | Select families |
| selectInd | Select individuals |
| selectOP | Select open pollinating plants |
| selectWithinFam | Select individuals within families |
| self | Self individuals |
| selIndex | Selection index |
| selInt | Selection intensity |
| setEBV | Set EBV |
| setPheno | Set phenotypes |
| setPhenoGCA | Set GCA as phenotype |
| 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 |
| smithHazel | Calculate Smith-Hazel weights |
| 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 |
| 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 |
| [-method | Hybrid population |
| [-method | Raw population with genetic map |
| [-method | Population |
| [-method | Raw Population |