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README

The AlphaSimR website is currently under development and has only been made available for testing at this time. This page will change when the website is ready for widespread use.

Publication

Gaynor, R. Chris, Gregor Gorjanc, and John M. Hickey. 2021. AlphaSimR: an R package for breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.

Download

AlphaSimR is available on CRAN.

To install use:

install.packages('AlphaSimR')

The development version of AlphaSimR (potentially unstable) can be accessed from the devel branch on GitHub.

To install use:

devtools::install_github(repo="gaynorr/AlphaSimR@devel")

To install with vignettes use:

devtools::install_github(repo="gaynorr/AlphaSimR@devel", build_vignettes=TRUE)

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Version

Install

install.packages('AlphaSimR')

Monthly Downloads

1,228

Version

1.2

License

MIT + file LICENSE

Issues

38

Pull Requests

2

Stars

53

Forks

23

Maintainer

Chris Gaynor

Last Published

June 15th, 2022

Functions in AlphaSimR (1.2)

RRBLUP2

RR-BLUP Model 2
RRBLUPMemUse

RRBLUP Memory Usage
RRBLUP_SCA

RR-BLUP SCA Model
Pop-class

Population
RRBLUP

RR-BLUP Model
NamedMapPop-class

Raw population with genetic map and id
MegaPop-class

Mega-Population
MapPop-class

Raw population with genetic map
LociMap-class

Loci metadata
AlphaSimR-package

AlphaSimR: Breeding Program Simulations
RRBLUP_SCA2

RR-BLUP SCA Model 2
HybridPop-class

Hybrid population
SimParam

Simulation parameters
TraitA-class

Additive trait
TraitAG-class

Additive and GxE trait
RRBLUP_GCA2

RR-BLUP GCA Model 2
RRBLUP_GCA

RR-BLUP GCA Model
getQtlMap

Get QTL genetic map
bv

Breeding value
attrition

Lose individuals at random
getSnpMap

Get SNP genetic map
cChr

Combine MapPop chromosomes
aa

Additive-by-additive epistatic deviations
makeDH

Generates DH lines
meanG

Mean genetic values
TraitADEG-class

Additive, dominance, epistasis, and GxE trait
TraitADE-class

Additive, dominance, and epistatic trait
RRBLUP_D2

RR-BLUP with Dominance Model 2
RRBLUP_D

RR-BLUP Model with Dominance
TraitAD-class

Additive and dominance trait
TraitADG-class

Additive, dominance and GxE trait
genicVarA

Additive genic variance
RRsol-class

RR-BLUP Solution
genicVarD

Dominance genic variance
calcGCA

Calculate GCA
getNumThreads

Number of available threads
TraitAEG-class

Additive, epistasis and GxE trait
ebv

Estimated breeding value
RawPop-class

Raw Population
TraitAE-class

Additive and epistatic trait
doubleGenome

Double the ploidy of individuals
getMisc

Get miscelaneous information in a population
editGenome

Edit genome
gv

Genetic value
hybridCross

Hybrid crossing
editGenomeTopQtl

Edit genome - the top QTL
newMapPop

New MapPop
nInd

Number of individuals
pullMarkerGeno

Pull marker genotypes
importInbredGeno

Import inbred, diploid genotypes
isFemale

Test if individuals of a population are female or male
genicVarAA

Additive-by-additive genic variance
TraitA2-class

Sex specific additive trait
newMegaPop

Create new Mega Population
popVar

Population variance
makeCross

Make designed crosses
runMacs2

Alternative wrapper for MaCS
sampleHaplo

Sample haplotypes from a MapPop
pullIbdHaplo

Pull IBD haplotypes
genicVarG

Total genic variance
makeCross2

Make designed crosses
newPop

Create new population
setMisc

Set miscelaneous information in a population
setEBV

Set EBV
pullMarkerHaplo

Pull marker haplotypes
meanP

Mean phenotypic values
mergeGenome

Combine genomes of individuals
pullQtlHaplo

Pull QTL haplotypes
pullQtlGeno

Pull QTL genotypes
dd

Dominance deviations
fastRRBLUP

Fast RR-BLUP
.newPop

Create new population (internal)
TraitA2D-class

Sex specific additive and dominance trait
genParam

Sumarize genetic parameters
solveRRBLUP_EM2

Solve RR-BLUP with EM and 2 random effects
pullSegSiteHaplo

Pull seg site haplotypes
pullSegSiteGeno

Pull segregating site genotypes
importGenMap

Import genetic map
importHaplo

Import haplotypes
setPheno

Set phenotypes
randCross2

Make random crosses
mutate

Add Random Mutations
selIndex

Selection index
mergePops

Merge list of populations
solveUVM

Solve Univariate Model
solveRRBLUP_EM3

Solve RR-BLUP with EM and 3 random effects
transMat

Linear transformation matrix
pedigreeCross

Pedigree cross
quickHaplo

Quick founder haplotype simulation
pheno

Phenotype
setPhenoGCA

Set GCA as phenotype
pullSnpGeno

Pull SNP genotypes
reduceGenome

Create individuals with reduced ploidy
selectInd

Select individuals
randCross

Make random crosses
selectOP

Select open pollinating plants
pullSnpHaplo

Pull SNP haplotypes
solveMKM

Solve Multikernel Model
selInt

Selection intensity
setPhenoProgTest

Set progeny test as phenotype
varG

Total genetic variance
smithHazel

Calculate Smith-Hazel weights
resetPop

Reset population
selectWithinFam

Select individuals within families
runMacs

Create founder haplotypes using MaCS
writePlink

Writes a Pop-class as PLINK files
solveMVM

Solve Multivariate Model
selectCross

Select and randomly cross
solveRRBLUP

Solve RR-BLUP
varP

Phenotypic variance
selectFam

Select families
writeRecords

Write data records
self

Self individuals
solveRRBLUPMK

Solve Multikernel RR-BLUP
varAA

Additive-by-additive epistatic variance
solveRRBLUP_EM

Solve RR-BLUP with EM
varA

Additive variance
usefulness

Usefulness criterion
solveRRBLUPMV

Solve Multivariate RR-BLUP
varD

Dominance variance