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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

1,482

Version

1.4.2

License

MIT + file LICENSE

Issues

34

Pull Requests

2

Stars

48

Forks

21

Maintainer

Chris Gaynor

Last Published

March 27th, 2023

Functions in AlphaSimR (1.4.2)

NamedMapPop-class

Raw population with genetic map and id
RRBLUPMemUse

RRBLUP Memory Usage
LociMap-class

Loci metadata
MegaPop-class

Mega-Population
RRBLUP

RR-BLUP Model
AlphaSimR-package

AlphaSimR: Breeding Program Simulations
RRsol-class

RR-BLUP Solution
RRBLUP_D

RR-BLUP Model with Dominance
RRBLUP_GCA2

RR-BLUP GCA Model 2
TraitA-class

Additive trait
RRBLUP_SCA2

RR-BLUP SCA Model 2
RawPop-class

Raw Population
RRBLUP_GCA

RR-BLUP GCA Model
RRBLUP_SCA

RR-BLUP SCA Model
SimParam

Simulation parameters
RRBLUP_D2

RR-BLUP with Dominance Model 2
TraitAG-class

Additive and GxE trait
TraitAEG-class

Additive, epistasis and GxE trait
TraitA2-class

Sex specific additive trait
TraitAD-class

Additive and dominance trait
TraitADEG-class

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

Additive, dominance, and epistatic trait
aa

Additive-by-additive epistatic deviations
TraitAE-class

Additive and epistatic trait
TraitA2D-class

Sex specific additive and dominance trait
calcGCA

Calculate GCA
dd

Dominance deviations
cChr

Combine MapPop chromosomes
bv

Breeding value
genicVarAA

Additive-by-additive genic variance
attrition

Lose individuals at random
addSegSite

Add segregating site to MapPop
TraitADG-class

Additive, dominance and GxE trait
getMisc

Get miscelaneous information in a population
getNumThreads

Number of available threads
isFemale

Test if individuals of a population are female or male
isPop

Test if object is of a Population class
importHaplo

Import haplotypes
importInbredGeno

Import inbred, diploid genotypes
genicVarD

Dominance genic variance
fastRRBLUP

Fast RR-BLUP
getQtlMap

Get QTL genetic map
editGenomeTopQtl

Edit genome - the top QTL
getPed

Get pedigree
ebv

Estimated breeding value
editGenome

Edit genome
getSnpMap

Get SNP genetic map
gv

Genetic value
genicVarA

Additive genic variance
mutate

Add Random Mutations
genicVarG

Total genic variance
nInd

Number of individuals
importGenMap

Import genetic map
genParam

Sumarize genetic parameters
mergePops

Merge list of populations
makeDH

Generates DH lines
newPop

Create new population
getGenMap

Get genetic map
hybridCross

Hybrid crossing
pedigreeCross

Pedigree cross
meanG

Mean genetic values
newEmptyPop

Creates an empty population
pheno

Phenotype
makeCross

Make designed crosses
makeCross2

Make designed crosses
reduceGenome

Create individuals with reduced ploidy
newMapPop

New MapPop
newMegaPop

Create new Mega Population
resetPop

Reset population
doubleGenome

Double the ploidy of individuals
.newPop

Create new population (internal)
meanP

Mean phenotypic values
runMacs

Create founder haplotypes using MaCS
pullSnpGeno

Pull SNP genotypes
runMacs2

Alternative wrapper for MaCS
pullSegSiteHaplo

Pull seg site haplotypes
popVar

Population variance
randCross

Make random crosses
selectFam

Select families
randCross2

Make random crosses
mergeGenome

Combine genomes of individuals
quickHaplo

Quick founder haplotype simulation
pullSnpHaplo

Pull SNP haplotypes
selectOP

Select open pollinating plants
pullQtlGeno

Pull QTL genotypes
pullMarkerHaplo

Pull marker haplotypes
selectWithinFam

Select individuals within families
setEBV

Set EBV
self

Self individuals
sampleHaplo

Sample haplotypes from a MapPop
selIndex

Selection index
setMisc

Set miscelaneous information in a population
setMarkerHaplo

Set marker haplotypes
selectInd

Select individuals
varA

Additive variance
usefulness

Usefulness criterion
setPhenoProgTest

Set progeny test as phenotype
setPheno

Set phenotypes
varD

Dominance variance
varAA

Additive-by-additive epistatic variance
transMat

Linear transformation matrix
varG

Total genetic variance
solveUVM

Solve Univariate Model
smithHazel

Calculate Smith-Hazel weights
solveRRBLUPMK

Solve Multikernel RR-BLUP
setPhenoGCA

Set GCA as phenotype
varP

Phenotypic variance
solveRRBLUP

Solve RR-BLUP
solveMVM

Solve Multivariate Model
solveRRBLUP_EM2

Solve RR-BLUP with EM and 2 random effects
pullIbdHaplo

Pull IBD haplotypes
pullSegSiteGeno

Pull segregating site genotypes
solveRRBLUP_EM3

Solve RR-BLUP with EM and 3 random effects
selectCross

Select and randomly cross
selInt

Selection intensity
solveMKM

Solve Multikernel Model
pullMarkerGeno

Pull marker genotypes
pullQtlHaplo

Pull QTL haplotypes
writeRecords

Write data records
solveRRBLUPMV

Solve Multivariate RR-BLUP
writePlink

Writes a Pop-class as PLINK files
solveRRBLUP_EM

Solve RR-BLUP with EM
Pop-class

Population
RRBLUP2

RR-BLUP Model 2
MapPop-class

Raw population with genetic map
HybridPop-class

Hybrid population