Man pages for AlphaSimR
Breeding Program Simulations
| aa | Additive-by-additive epistatic deviations |
| addError | Add residual error to genetic values |
| addSegSite | Add segregating site to MapPop |
| AlphaSimR-package | AlphaSimR: Breeding Program Simulations |
| asCategorical | Convert a normal (Gaussian) trait to an ordered categorical... |
| attrition | Lose individuals at random |
| bv | Breeding value |
| calcGCA | Calculate GCA |
| calcPheno | Calculate phenotypes |
| cChr | Combine MapPop chromosomes |
| checkSexes | Find individuals of desired sex |
| convertTraitsToNames | Convert traits to a vector of names |
| dd | Dominance deviations |
| dot-newPop | Create new population |
| doubleGenome | Double the ploidy of individuals |
| ebv | Estimated breeding value |
| editGenome | Edit genome |
| editGenomeTopQtl | Edit genome - the top QTL |
| fastRRBLUP | Fast RR-BLUP |
| findLociMapSuperset | Find LociMap superset |
| findQtlIndex | Find trait QTL index |
| genicVarA | Additive genic variance |
| genicVarAA | Additive-by-additive genic variance |
| genicVarD | Dominance genic variance |
| genicVarG | Total genic variance |
| genParam | Sumarize genetic parameters |
| getCandidates | Identify candidate individuals |
| getFam | Determine families |
| getGenMap | Get genetic map |
| getLociNames | Retrieves marker names from genMap |
| getNumThreads | Number of available threads |
| getPed | Get pedigree |
| getQtlMap | Get QTL genetic map |
| getResponse | Returns a vector response from a population |
| getSnpMap | Get SNP genetic map |
| gv | Genetic value |
| hybridCross | Hybrid crossing |
| HybridPop-class | Hybrid population |
| 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 |
| LociMap-class | Loci metadata |
| makeCross | Make designed crosses |
| makeCross2 | Make designed crosses |
| makeDH | Generates DH lines |
| mapLoci | Finds positions of loci by marker name |
| MapPop-class | Raw population with genetic map |
| 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 |
| MultiPop-class | Multi-Population |
| mutate | Add Random Mutations |
| NamedMapPop-class | Raw population with genetic map and id |
| newEmptyPop | Creates an empty population |
| newMapPop | New MapPop |
| newMultiPop | Create new Multi Population |
| newPop | Create new population |
| nInd | Number of individuals |
| parentAverage | Calculate parent average |
| pedigreeCross | Pedigree cross |
| pheno | Phenotype |
| Pop-class | Population |
| popVar | Population variance |
| popVarCpp | 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 |
| RawPop-class | Raw Population |
| reduceGenome | Create individuals with reduced ploidy |
| resetPop | Reset population |
| rnormWithSeed | Sample normal deviates using a seed |
| RRBLUP | RR-BLUP Model |
| RRBLUP2 | RR-BLUP Model 2 |
| 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 |
| RRBLUPMemUse | RRBLUP Memory Usage |
| RRBLUP_SCA | RR-BLUP SCA Model |
| RRBLUP_SCA2 | RR-BLUP SCA Model 2 |
| RRsol-class | RR-BLUP Solution |
| runMacs | Create founder haplotypes using MaCS |
| runMacs2 | Alternative wrapper for MaCS |
| sampAddEff | Sample additive effects |
| sampDomEff | Sample dominance effects |
| sampEpiEff | Sample epistatic effects |
| sampleHaplo | Sample haplotypes from a MapPop |
| selectCross | Select and randomly cross |
| selectFam | Select families |
| selectInd | Select individuals |
| selectLoci | Find loci on specific chromosomes |
| selectOP | Select open pollinating plants |
| selectWithinFam | Select individuals within families |
| self | Self individuals |
| selIndex | Selection index |
| selInt | Selection intensity |
| setEBV | Set estimated breeding values (EBV) |
| setMarkerHaplo | Set marker haplotypes |
| setPheno | Set phenotypes |
| setPhenoGCA | Set GCA as phenotype |
| setPhenoProgTest | Set progeny test as phenotype |
| SimParam | Simulation parameters |
| smithHazel | Calculate Smith-Hazel weights |
| solveMKM | Solve Multikernel Model |
| solveMVM | Solve Multivariate Model |
| solveRRBLUP | Solve 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 |
| solveRRBLUPMK | Solve Multikernel RR-BLUP |
| solveRRBLUPMV | Solve Multivariate RR-BLUP |
| solveUVM | Solve Univariate Model |
| TraitA2-class | Sex specific additive trait |
| TraitA2D-class | Sex specific additive and dominance 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 |
| transMat | Linear transformation matrix |
| 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 |
