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This package is currently under development. A manuscript detailing its use and the theory behind its operation is in preparation.

'AlphaSimR' is available on both CRAN and Bitbucket. The most recent version will be on Bitbucket and it can be downloaded and installed using the 'devtools' library and the following command: devtools::install_bitbucket("hickeyjohnteam/AlphaSimR")

Installing from Bitbucket requires the following libraries: 'R6', 'Rcpp', 'RcppArmadillo', and 'BH'.

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Version

Install

install.packages('AlphaSimR')

Monthly Downloads

1,482

Version

0.11.0

License

MIT + file LICENSE

Maintainer

Chris Gaynor

Last Published

October 11th, 2019

Functions in AlphaSimR (0.11.0)

MapPop-class

Raw population with genetic map
SimParam_new

Create new simulation
SimParam_manAddTrait

Manually add trait
RRBLUP_SCA

RR-BLUP SCA Model
RRBLUP_SCA2

RR-BLUP SCA Model 2
SimParam_setCorE

Set correlated error variance
RRBLUP_GCA

RR-BLUP GCA Model
SimParam_setGender

Set gender in simulation
RRBLUP_GCA2

RR-BLUP GCA Model 2
SimParam_addTraitA

Add additive traits
SimParam_addStructuredSnpChips

Add Structured SNP chips
RRsol-class

RR-BLUP Solution
SimParam_restrSegSites

Restrict segregating sites
SimParam_resetPed

Reset pedigree
SimParam_switchFemaleMap

Switch female genetic map
RawPop-class

Raw Population
SimParam_addTraitAEG

Add additive and epistasis GxE traits
SimParam_addTraitAE

Add additive and epistasis traits
SimParam_switchSnpChip

Switch SNP chip
SimParam_addSnpChip

Add SNP chip
SimParam

Simulation parameters
SimParam_addTraitAG

Add additive GxE traits
SimParam_manAddSnpChip

Manually add SNP chip
SimParam_switchGenMap

Switch genetic map
SimParam_switchTrait

Switch trait
SimParam_switchFounderPop

Switch founder population
randCross2

Make random crosses
mergePops

Merge list of populations
runMacs

Create founder haplotypes using MaCS
mutate

Add Random Mutations
dd

Dominance deviations
resetPop

Reset population
TraitA2D-class

Gender specific additive and dominance trait
randCross

Make random crosses
calcGCA

Calculate GCA
SimParam_addTraitADEG

Add an additive, dominance, and epistasis GxE trait
SimParam_switchMaleMap

Switch male genetic map
SimParam_removeFounderPop

Remove founder population
SimParam_addTraitAD

Add additive and dominance traits
SimParam_addTraitADE

Add additive, dominance and epistasis traits
SimParam_removeSnpChip

Remove SNP chip
SimParam_setMeiosis

Set meiosis parameters
TraitA-class

Additive trait
TraitA2-class

Gender specific additive trait
SimParam_setTrackPed

Set pedigree tracking
aa

Additive-by-additive epistatic deviations
TraitADE-class

Additive, dominance, and epistatic trait
TraitAD-class

Additive and dominance trait
SimParam_removeTrait

Remove trait
SimParam_rescaleTraits

Rescale traits
SimParam_addTraitADG

Add an additive and dominance GxE trait
TraitAEG-class

Additive, epistasis and GxE trait
TraitAG-class

Additive and GxE trait
bv

Breeding value
ebv

Estimated breeding value
editGenome

Edit genome
TraitADEG-class

Additive, dominance, epistasis, and GxE trait
genParam

Sumarize genetic parameters
selectWithinFam

Select individuals within families
self

Self individuals
SimParam_setVarE

Set simulation error variance
TraitAE-class

Additive and epistatic trait
SimParam_setTrackRec

Set recombination tracking
hybridCross

Hybrid crossing
TraitADG-class

Additive, dominance and GxE trait
genicVarA

Additive genic variance
getSnpMap

Get SNP genetic map
editGenomeTopQtl

Edit genome - the top QTL
gv

Genetic value
meanG

Mean genetic values
genicVarAA

Additive-by-additive genic variance
makeCross2

Make designed crosses
makeDH

Generates DH lines
genicVarD

Dominance genic variance
fastRRBLUP

Fast RR-BLUP
pullIbdHaplo

Pull Identity By Descent (IBD) haplotypes
pheno

Phenotype
makeCross

Make designed crosses
popVar

Population variance
meanP

Mean phenotypic values
newMapPop

New MapPop
pullSegSiteGeno

Pull seg site genotypes
selectInd

Select individuals
pullQtlHaplo

Pull QTL haplotypes
nInd

Number of individuals
quickHaplo

Quick founder haplotype simulation
pullSnpHaplo

Pull SNP haplotypes
genicVarG

Total genic variance
runMacs2

Alternative wrapper for MaCS
getQtlMap

Get QTL genetic map
selectOP

Select open pollinating plants
pullMultipleSnpGeno

Pull SNP genotype for multiple snp chips
pedigreeCross

Pedigree cross
newPop

Create new Population
pullSegSiteHaplo

Pull seg site haplotypes
pullSnpGeno

Pull SNP genotype
selectCross

Select and randomly cross
setPhenoGCA

Set GCA as phenotype
selectFam

Select families
selInt

Selection intensity
selIndex

Selection index
pullQtlGeno

Pull QTL genotype
pullMultipleSnpHaplo

Pull SNP haplotypes for multiple chips
usefulness

Usefulness criterion
varA

Additive variance
setEBV

Set EBV
setPheno

Set phenotypes
sampleHaplo

Sample haplotypes from a MapPop
smithHazel

Calculate Smith-Hazel weights
varAA

Additive-by-additive epistatic variance
writePlink

Writes a Pop-class as PLINK files
varG

Total genetic variance
varP

Phenotypic variance
varD

Dominance variance
writeRecords

Write data records
RRBLUPMemUse

RRBLUP Memory Usage
RRBLUP_D2

RR-BLUP with Dominance Model 2
Pop-class

Population
HybridPop-class

Hybrid population
LociMap-class

Loci metadata
AlphaSimR

AlphaSimR: Breeding Program Simulations
RRBLUP2

RR-BLUP Model 2
RRBLUP_D

RR-BLUP Model with Dominance
RRBLUP

RR-BLUP Model