# Breeding Program Simulations

## Documentation for package ‘AlphaSimR’ version 2.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N P Q R S T U V W misc

## -- A --

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

## -- B --

bv | Breeding value

## -- C --

c-method | Hybrid population
c-method | Raw population with genetic map
c-method | Multi-Population
c-method | Raw population with genetic map and id
c-method | Population
c-method | Raw Population
calcGCA | Calculate GCA
cChr | Combine MapPop chromosomes

## -- D --

dd | Dominance deviations
doubleGenome | Double the ploidy of individuals

## -- E --

ebv | Estimated breeding value
editGenome | Edit genome
editGenomeTopQtl | Edit genome - the top QTL

## -- F --

fastRRBLUP | Fast RR-BLUP

## -- G --

genicVarA | Additive genic variance
genicVarAA | Additive-by-additive genic variance
genicVarD | Dominance genic variance
genicVarG | Total genic variance
genParam | Sumarize genetic parameters
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

## -- H --

hybridCross | Hybrid crossing
HybridPop-class | Hybrid population

## -- I --

importGenMap | Import genetic map
importHaplo | Import haplotypes
importInbredGeno | Import inbred, diploid genotypes
isFemale | Test if individuals of a population are female or male
isHybridPop | Hybrid population
isMale | Test if individuals of a population are female or male
isMapPop | Raw population with genetic map
isMultiPop | Multi-Population
isNamedMapPop | Raw population with genetic map and id
isPop | Test if object is of a Population class
isRawPop | Raw Population

## -- L --

length-method | Multi-Population
length-method | Population
LociMap-class | Loci metadata

## -- M --

makeCross | Make designed crosses
makeCross2 | Make designed crosses
makeDH | Generates DH lines
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

## -- N --

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

## -- P --

parentAverage | Calculate parent average
pedigreeCross | Pedigree cross
pheno | Phenotype
Pop-class | Population
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

## -- Q --

quickHaplo | Quick founder haplotype simulation

## -- R --

randCross | Make random crosses
randCross2 | Make random crosses
RawPop-class | Raw Population
reduceGenome | Create individuals with reduced ploidy
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
RRBLUP_SCA2 | RR-BLUP SCA Model 2
RRsol-class | RR-BLUP Solution
runMacs | Create founder haplotypes using MaCS
runMacs2 | Alternative wrapper for MaCS

## -- S --

sampleHaplo | Sample haplotypes from a MapPop
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 estimated breeding values (EBV)
setMarkerHaplo | Set marker haplotypes
setPheno | Set phenotypes
setPhenoGCA | Set GCA as phenotype
setPhenoProgTest | Set progeny test as phenotype
show-method | Population
show-method | Raw Population
SimParam | Simulation parameters
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

## -- T --

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

## -- U --

usefulness | Usefulness criterion

## -- V --

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

## -- W --

writePlink | Writes a Pop-class as PLINK files
writeRecords | Write data records

## -- misc --

[-method | Hybrid population
[-method | Raw population with genetic map
[-method | Multi-Population
[-method | Raw population with genetic map and id
[-method | Population
[-method | Raw Population
[[-method | Multi-Population