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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

0.10.0

License

MIT + file LICENSE

Maintainer

Chris Gaynor

Last Published

March 15th, 2019

Functions in AlphaSimR (0.10.0)

HybridPop-class

Hybrid population
RRBLUPMemUse

RRBLUP Memory Usage
LociMap-class

Loci metadata
RRBLUP_D

RR-BLUP Model with Dominance
RRBLUP

RR-BLUP Model
RawPop-class

Raw Population
RRBLUP2

RR-BLUP Model 2
SCAsol-class

RR-BLUP SCA Solution
SimParam_addTraitADE

Add additive, dominance and epistasis traits
SimParam_addTraitAD

Add additive and dominance traits
SimParam_manAddTrait

Manually add trait
SimParam

Simulation parameters
SimParam_new

Create new simulation
SimParam_switchFemaleMap

Switch female genetic map
SimParam_switchFounderPop

Switch founder population
AlphaSimR

AlphaSimR: Breeding Program Simulations
SimParam_addTraitADEG

Add an additive, dominance, and epistasis GxE trait
SimParam_addSnpChip

Add SNP chip
SimParam_addStructuredSnpChips

Add Structured SNP chips
SimParam_addTraitA

Add additive traits
TraitA-class

Additive trait
GCAsol-class

RR-BLUP GCA Solution
SimParam_removeTrait

Remove trait
RRBLUP_GCA2

RR-BLUP GCA Model 2
RRBLUP_SCA

RR-BLUP SCA Model
SimParam_setRecRatio

Set gender specific recombination
SimParam_setTrackPed

Set pedigree tracking
SimParam_addTraitADG

Add an additive and dominance GxE trait
TraitAD-class

Additive and dominance trait
MapPop-class

Raw population with genetic map
Pop-class

Population
SimParam_resetPed

Reset pedigree
TraitADE-class

Additive, dominance, and epistatic trait
SimParam_rescaleTraits

Rescale traits
SimParam_restrSegSites

Restrict segregating sites
makeCross2

Make designed crosses
pedigreeCross

Pedigree cross
makeDH

Generates DH lines
SimParam_switchGenMap

Switch genetic map
pheno

Phenotype
RRDsol-class

RR-BLUP Solution with Dominance
SimParam_setTrackRec

Set recombination tracking
SimParam_switchMaleMap

Switch male genetic map
SimParam_setVarE

Set simulation error variance
RRsol-class

RR-BLUP Solution
randCross

Make random crosses
quickHaplo

Quick founder haplotype simulation
selectOP

Select open pollinating plants
TraitADEG-class

Additive, dominance, epistasis, and GxE trait
genicVarAA

Additive-by-additive genic variance
selectWithinFam

Select individuals within families
genicVarD

Dominance genic variance
RRBLUP_D2

RR-BLUP with Dominance Model 2
newMapPop

New MapPop
aa

Additive-by-additive epistatic deviations
newPop

Create new Population
bv

Breeding value
RRBLUP_GCA

RR-BLUP GCA Model
genParam

Sumarize genetic parameters
TraitAEG-class

Additive, epistasis and GxE trait
SimParam_addTraitAE

Add additive and epistasis traits
setPheno

Set phenotypes
genicVarA

Additive genic variance
TraitAG-class

Additive and GxE trait
editGenomeTopQtl

Edit genome - the top QTL
fastRRBLUP

Fast RR-BLUP
SimParam_addTraitAEG

Add additive and epistasis GxE traits
SimParam_addTraitAG

Add additive GxE traits
SimParam_removeFounderPop

Remove founder population
SimParam_manAddSnpChip

Manually add SNP chip
genicVarG

Total genic variance
setPhenoGCA

Set GCA as phenotype
getQtlMap

Get QTL genetic map
randCross2

Make random crosses
SimParam_setCorE

Set correlated error variance
SimParam_setGender

Set gender in simulation
SimParam_removeSnpChip

Remove SNP chip
SimParam_switchSnpChip

Switch SNP chip
pullMultipleSnpGeno

Pull SNP genotype for multiple snp chips
SimParam_switchTrait

Switch trait
TraitADG-class

Additive, dominance and GxE trait
TraitAE-class

Additive and epistatic trait
resetPop

Reset population
selInt

Selection intensity
selectCross

Select and randomly cross
varD

Dominance variance
ebv

Estimated breeding value
editGenome

Edit genome
varG

Total genetic variance
varP

Phenotypic variance
calcGCA

Calculate GCA
getSnpMap

Get SNP genetic map
gv

Genetic value
pullMultipleSnpHaplo

Pull SNP haplotypes for multiple chips
pullQtlHaplo

Pull QTL haplotypes
pullQtlGeno

Pull QTL genotype
runMacs

Create founder haplotypes using MaCS
dd

Dominance deviations
pullSegSiteGeno

Pull seg site genotypes
hybridCross

Hybrid crossing
makeCross

Make designed crosses
meanG

Mean genetic values
writePlink

Writes a Pop-class as PLINK files
meanP

Mean phenotypic values
runMacs2

Alternative wrapper for MaCS
pullSegSiteHaplo

Pull seg site haplotypes
self

Self individuals
selectFam

Select families
setEBV

Set EBV
mergePops

Merge list of populations
nInd

Number of individuals
pullSnpGeno

Pull SNP genotype
selectInd

Select individuals
popVar

Population variance
smithHazel

Calculate Smith-Hazel weights
pullIbdHaplo

Pull Identity By Descent (IBD) haplotypes
pullSnpHaplo

Pull SNP haplotypes
sampleHaplo

Sample haplotypes from a MapPop
selIndex

Selection index
varA

Additive variance
varAA

Additive-by-additive epistatic variance
usefulness

Usefulness criterion
writeRecords

Write data records