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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

0.11.1

License

MIT + file LICENSE

Maintainer

Chris Gaynor

Last Published

January 13th, 2020

Functions in AlphaSimR (0.11.1)

AlphaSimR

AlphaSimR: Breeding Program Simulations
Pop-class

Population
RRBLUP

RR-BLUP Model
LociMap-class

Loci metadata
RRBLUPMemUse

RRBLUP Memory Usage
RRBLUP_D

RR-BLUP Model with Dominance
MapPop-class

Raw population with genetic map
RRBLUP_D2

RR-BLUP with Dominance Model 2
HybridPop-class

Hybrid population
RRBLUP2

RR-BLUP Model 2
RRBLUP_SCA

RR-BLUP SCA Model
SimParam_addStructuredSnpChips

Add Structured SNP chips
SimParam_restrSegSites

Restrict segregating sites
SimParam_addTraitADE

Add additive, dominance and epistasis traits
SimParam_addTraitAD

Add additive and dominance traits
SimParam_resetPed

Reset pedigree
RRBLUP_GCA2

RR-BLUP GCA Model 2
RRBLUP_GCA

RR-BLUP GCA Model
RRsol-class

RR-BLUP Solution
SimParam_rescaleTraits

Rescale traits
TraitADG-class

Additive, dominance and GxE trait
TraitAE-class

Additive and epistatic trait
mergePops

Merge list of populations
genParam

Sumarize genetic parameters
genicVarAA

Additive-by-additive genic variance
SimParam_switchMaleMap

Switch male genetic map
SimParam_switchGenMap

Switch genetic map
RawPop-class

Raw Population
SimParam

Simulation parameters
RRBLUP_SCA2

RR-BLUP SCA Model 2
SimParam_addTraitAE

Add additive and epistasis traits
SimParam_switchTrait

Switch trait
runMacs2

Alternative wrapper for MaCS
SimParam_addTraitAEG

Add additive and epistasis GxE traits
SimParam_setMeiosis

Set meiosis parameters
SimParam_addTraitAG

Add additive GxE traits
SimParam_switchFemaleMap

Switch female genetic map
SimParam_setTrackPed

Set pedigree tracking
SimParam_manAddSnpChip

Manually add SNP chip
SimParam_switchFounderPop

Switch founder population
aa

Additive-by-additive epistatic deviations
SimParam_addTraitA

Add additive traits
randCross

Make random crosses
resetPop

Reset population
genicVarD

Dominance genic variance
genicVarA

Additive genic variance
SimParam_addTraitADEG

Add an additive, dominance, and epistasis GxE trait
TraitA-class

Additive trait
pullSegSiteHaplo

Pull seg site haplotypes
SimParam_switchSnpChip

Switch SNP chip
pullQtlHaplo

Pull QTL haplotypes
meanG

Mean genetic values
pullSegSiteGeno

Pull seg site genotypes
doubleGenome

Double the ploidy of individuals
meanP

Mean phenotypic values
bv

Breeding value
hybridCross

Hybrid crossing
dd

Dominance deviations
writeRecords

Write data records
runMacs

Create founder haplotypes using MaCS
makeCross

Make designed crosses
SimParam_removeTrait

Remove trait
TraitADEG-class

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

Additive, dominance, and epistatic trait
calcGCA

Calculate GCA
reduceGenome

Create individuals with reduced ploidy
SimParam_addTraitADG

Add an additive and dominance GxE trait
self

Self individuals
randCross2

Make random crosses
setEBV

Set EBV
mutate

Add Random Mutations
cChr

Combine MapPop chromosomes
editGenome

Edit genome
pullSnpHaplo

Pull SNP haplotypes
selectOP

Select open pollinating plants
makeCross2

Make designed crosses
makeDH

Generates DH lines
SimParam_setCorE

Set correlated error variance
gv

Genetic value
SimParam_manAddTrait

Manually add trait
SimParam_addSnpChip

Add SNP chip
SimParam_new

Create new simulation
newPop

Create new Population
varA

Additive variance
varAA

Additive-by-additive epistatic variance
SimParam_removeSnpChip

Remove SNP chip
smithHazel

Calculate Smith-Hazel weights
TraitAG-class

Additive and GxE trait
TraitAEG-class

Additive, epistasis and GxE trait
SimParam_removeFounderPop

Remove founder population
TraitA2-class

Gender specific additive trait
ebv

Estimated breeding value
pheno

Phenotype
pedigreeCross

Pedigree cross
selInt

Selection intensity
quickHaplo

Quick founder haplotype simulation
popVar

Population variance
getQtlMap

Get QTL genetic map
selectInd

Select individuals
genicVarG

Total genic variance
selectFam

Select families
varP

Phenotypic variance
pullSnpGeno

Pull SNP genotype
writePlink

Writes a Pop-class as PLINK files
selectCross

Select and randomly cross
selectWithinFam

Select individuals within families
usefulness

Usefulness criterion
fastRRBLUP

Fast RR-BLUP
editGenomeTopQtl

Edit genome - the top QTL
SimParam_setGender

Set gender in simulation
SimParam_setTrackRec

Set recombination tracking
getSnpMap

Get SNP genetic map
SimParam_setVarE

Set simulation error variance
TraitA2D-class

Gender specific additive and dominance trait
nInd

Number of individuals
TraitAD-class

Additive and dominance trait
pullIbdHaplo

Pull Identity By Descent (IBD) haplotypes
setPhenoGCA

Set GCA as phenotype
sampleHaplo

Sample haplotypes from a MapPop
selIndex

Selection index
setPheno

Set phenotypes
newMapPop

New MapPop
varG

Total genetic variance
varD

Dominance variance
pullQtlGeno

Pull QTL genotype