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README

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

1,146

Version

0.9.0

License

MIT + file LICENSE

Maintainer

Chris Gaynor

Last Published

February 7th, 2019

Functions in AlphaSimR (0.9.0)

RRBLUP

RR-BLUP Model
SimParam_addTraitADG

Add an additive and dominance GxE trait
GCAsol-class

RR-BLUP GCA Solution
SimParam_addSnpChip

Add SNP chip
SimParam_switchMaleMap

Switch male genetic map
SimParam_switchSnpChip

Switch SNP chip
SimParam_addTraitAG

Add additive GxE traits
SimParam_addStructuredSnpChips

Add Structured SNP chips
SimParam_removeSnpChip

Remove SNP chip
SCAsol-class

RR-BLUP SCA Solution
genicVarG

Total genic variance
MapPop-class

Raw population with genetic map
SimParam_removeTrait

Remove trait
Pop-class

Population
SimParam_setTrackPed

Set pedigree tracking
HybridPop-class

Hybrid population
RRBLUPMemUse

RRBLUP Memory Usage
gv

Genetic value
SimParam

Simulation parameters
SimParam_setTrackRec

Set recombination tracking
SimParam_new

Create new simulation
SimParam_removeFounderPop

Remove founder population
SimParam_setVarE

Set simulation error variance
SimParam_switchFemaleMap

Switch female genetic map
calcGCA

Calculate GCA
dd

Dominance deviations
newMapPop

New MapPop
SimParam_setGender

Set gender in simulation
newPop

Create new Population
SimParam_switchTrait

Switch trait
makeCross2

Make designed crosses
RRBLUP_D

RR-BLUP Model with Dominance
bv

Breeding value
TraitAG-class

Additive and GxE trait
SimParam_setRecRatio

Set gender specific recombination
makeDH

Generates DH lines
randCross2

Make random crosses
pullSegSiteGeno

Pull seg site genotypes
LociMap-class

Loci metadata
TraitA-class

Additive trait
RRsol-class

RR-BLUP Solution
pullSegSiteHaplo

Pull seg site haplotypes
makeCross

Make designed crosses
hybridCross

Hybrid crossing
popVar

Population variance
editGenome

Edit genome
ebv

Estimated breeding value
RRBLUP_GCA

RR-BLUP GCA Model
RRBLUP_GCA2

RR-BLUP GCA Model 2
meanG

Mean genetic values
meanP

Mean phenotypic values
sampleHaplo

Sample haplotypes from a MapPop
RawPop-class

Raw Population
selIndex

Selection index
SimParam_addTraitA

Add additive traits
pullIbdHaplo

Pull Identity By Descent (IBD) haplotypes
runMacs

Create founder haplotypes using MaCS
runMacs2

Alternative wrapper for MaCS
pullMultipleSnpGeno

Pull SNP genotype for multiple snp chips
resetPop

Reset population
selectFam

Select families
selectInd

Select individuals
SimParam_manAddSnpChip

Manually add SNP chip
SimParam_manAddTrait

Manually add trait
SimParam_rescaleTraits

Rescale traits
SimParam_resetPed

Reset pedigree
SimParam_switchFounderPop

Switch founder population
SimParam_switchGenMap

Switch genetic map
setPheno

Set phenotypes
setPhenoGCA

Set GCA as phenotype
SimParam_addTraitAD

Add additive and dominance traits
SimParam_restrSegSites

Restrict segregating sites
editGenomeTopQtl

Edit genome - the top QTL
genParam

Sumarize genetic parameters
trackHaploPop

Haplotype tracking population
smithHazel

Calculate Smith-Hazel weights
pedigreeCross

Pedigree cross
varP

Phenotypic variance
writePlink

Writes a Pop-class as PLINK files
SimParam_setCorE

Set correlated error variance
TraitAD-class

Additive and dominance trait
selInt

Selection intensity
pheno

Phenotype
selectCross

Select and randomly cross
pullMultipleSnpHaplo

Pull SNP haplotypes for multiple chips
quickHaplo

Quick founder haplotype simulation
varD

Dominance variance
varG

Total genetic variance
TraitADG-class

Additive, dominance and GxE trait
genicVarA

Additive genic variance
randCross

Make random crosses
genicVarD

Dominance genic variance
mergePops

Merge list of populations
selectOP

Select open pollinating plants
nInd

Number of individuals
selectWithinFam

Select individuals within families
usefulness

Usefulness criterion
varA

Additive variance
pullQtlGeno

Pull QTL genotype
pullQtlHaplo

Pull QTL haplotypes
pullSnpGeno

Pull SNP genotype
pullSnpHaplo

Pull SNP haplotypes
self

Self individuals
setEBV

Set EBV
writeRecords

Write data records
AlphaSimR

AlphaSimR: Breeding Program Simulations
RRBLUP2

RR-BLUP Model 2
RRBLUP_SCA

RR-BLUP SCA Model
RRDsol-class

RR-BLUP Solution with Dominance