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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

3,191

Version

0.12.1

License

MIT + file LICENSE

Maintainer

Chris Gaynor

Last Published

March 30th, 2020

Functions in AlphaSimR (0.12.1)

LociMap-class

Loci metadata
RRBLUPMemUse

RRBLUP Memory Usage
RRBLUP2

RR-BLUP Model 2
SimParam

Simulation parameters
AlphaSimR

AlphaSimR: Breeding Program Simulations
RRBLUP_GCA

RR-BLUP GCA Model
HybridPop-class

Hybrid population
TraitA-class

Additive trait
TraitAE-class

Additive and epistatic trait
RawPop-class

Raw Population
TraitAEG-class

Additive, epistasis and GxE trait
TraitA2D-class

Gender specific additive and dominance trait
TraitADEG-class

Additive, dominance, epistasis, and GxE trait
RRBLUP_D2

RR-BLUP with Dominance Model 2
RRBLUP_D

RR-BLUP Model with Dominance
TraitA2-class

Gender specific additive trait
calcGCA

Calculate GCA
dd

Dominance deviations
RRBLUP_GCA2

RR-BLUP GCA Model 2
TraitADG-class

Additive, dominance and GxE trait
RRBLUP

RR-BLUP Model
Pop-class

Population
RRBLUP_SCA

RR-BLUP SCA Model
TraitAD-class

Additive and dominance trait
RRBLUP_SCA2

RR-BLUP SCA Model 2
fastRRBLUP

Fast RR-BLUP
getSnpMap

Get SNP genetic map
getQtlMap

Get QTL genetic map
nInd

Number of individuals
pheno

Phenotype
genParam

Sumarize genetic parameters
genicVarD

Dominance genic variance
TraitADE-class

Additive, dominance, and epistatic trait
genicVarG

Total genic variance
newMapPop

New MapPop
bv

Breeding value
popVar

Population variance
runMacs2

Alternative wrapper for MaCS
cChr

Combine MapPop chromosomes
runMacs

Create founder haplotypes using MaCS
pullSegSiteGeno

Pull seg site genotypes
self

Self individuals
pullQtlHaplo

Pull QTL haplotypes
genicVarA

Additive genic variance
setEBV

Set EBV
genicVarAA

Additive-by-additive genic variance
TraitAG-class

Additive and GxE trait
pullSnpHaplo

Pull SNP haplotypes
quickHaplo

Quick founder haplotype simulation
makeCross2

Make designed crosses
pullIbdHaplo

Pull Identity By Descent (IBD) haplotypes
newPop

Create new Population
pedigreeCross

Pedigree cross
makeCross

Make designed crosses
aa

Additive-by-additive epistatic deviations
sampleHaplo

Sample haplotypes from a MapPop
pullQtlGeno

Pull QTL genotype
selIndex

Selection index
varA

Additive variance
varAA

Additive-by-additive epistatic variance
editGenome

Edit genome
editGenomeTopQtl

Edit genome - the top QTL
gv

Genetic value
ebv

Estimated breeding value
doubleGenome

Double the ploidy of individuals
makeDH

Generates DH lines
hybridCross

Hybrid crossing
meanP

Mean phenotypic values
selInt

Selection intensity
meanG

Mean genetic values
selectCross

Select and randomly cross
mutate

Add Random Mutations
mergePops

Merge list of populations
setPheno

Set phenotypes
randCross

Make random crosses
setPhenoGCA

Set GCA as phenotype
reduceGenome

Create individuals with reduced ploidy
randCross2

Make random crosses
resetPop

Reset population
writeRecords

Write data records
selectWithinFam

Select individuals within families
selectOP

Select open pollinating plants
varD

Dominance variance
pullSegSiteHaplo

Pull seg site haplotypes
mergeGenome

Combine genomes of individuals
pullSnpGeno

Pull SNP genotype
selectFam

Select families
varG

Total genetic variance
selectInd

Select individuals
usefulness

Usefulness criterion
writePlink

Writes a Pop-class as PLINK files
smithHazel

Calculate Smith-Hazel weights
varP

Phenotypic variance
MapPop-class

Raw population with genetic map
RRsol-class

RR-BLUP Solution