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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

1,482

Version

0.8.2

License

MIT + file LICENSE

Homepage

https://alphagenes.roslin.ed.ac.uk/wp/software/alphasimr/

Maintainer

Chris Gaynor

Last Published

October 15th, 2018

Functions in AlphaSimR (0.8.2)

HybridPop-class

Hybrid population

RR-BLUP Solution with Dominance

RR-BLUP Solution

SimParam_addTraitAD

Add additive and dominance traits

SimParam_addTraitADG

Add an additive and dominance GxE trait

SimParam_setTrackRec

Set recombination tracking

SimParam_setVarE

Set simulation error variance

RRBLUP Memory Usage

SimParam_switchGenMap

Switch genetic map

RR-BLUP Model with Dominance

SimParam_switchMaleMap

Switch male genetic map

Create new simulation

SimParam_manAddTrait

Manually add trait

Dominance deviations

SimParam_setRecRatio

Set gender specific recombination

AlphaSimR-package

AlphaSimR: Breeding Program Simulations

RR-BLUP GCA Model

Estimated breeding value

RR-BLUP GCA Solution

Create new Population

RR-BLUP SCA Model

pullMultipleSnpHaplo

Pull SNP haplotypes for multiple chips

Raw population with genetic map

SimParam_switchSnpChip

Switch SNP chip

SimParam_setTrackPed

Set pedigree tracking

Pull QTL genotype

RR-BLUP SCA Solution

SimParam_addStructuredSnpChips

Add Structured SNP chips

SimParam_removeTrait

SimParam_rescaleTraits

SimParam_addTraitAG

Add additive GxE traits

SimParam_manAddSnpChip

Manually add SNP chip

Pull SNP haplotypes

SimParam_resetPed

SimParam_addTraitA

Add additive traits

Quick founder haplotype simulation

Set GCA as phenotype

SimParam_switchTrait

Additive variance

Calculate Smith-Hazel weights

Sumarize genetic parameters

SimParam_restrSegSites

Restrict segregating sites

SimParam_setCorE

Set correlated error variance

Additive genic variance

Make designed crosses

SimParam_setGender

Set gender in simulation

Make designed crosses

RR-BLUP Model 2

Simulation parameters

Dominance variance

Additive and dominance trait

SimParam_addSnpChip

Population variance

Dominance genic variance

Total genic variance

Reset population

Create founder haplotypes using MaCS

selectWithinFam

Select individuals within families

SimParam_removeFounderPop

Remove founder population

SimParam_removeSnpChip

Remove SNP chip

Self individuals

SimParam_switchFemaleMap

Switch female genetic map

Hybrid crossing

Number of individuals

Writes a Pop-class as PLINK files

Write data records

editGenomeTopQtl

Edit genome - the top QTL

SimParam_switchFounderPop

Switch founder population

Mean phenotypic values

Merge list of populations

Pull QTL haplotypes

Additive, dominance and GxE trait

pullSegSiteGeno

Pull seg site genotypes

Alternative wrapper for MaCS

Sample haplotypes from a MapPop

Select individuals

Select open pollinating plants

Haplotype tracking population

Additive and GxE trait

Generates DH lines

Mean genetic values

pullSegSiteHaplo

Pull seg site haplotypes

Usefulness criterion

Pull Identity By Descent (IBD) haplotypes

pullMultipleSnpGeno

Pull SNP genotype for multiple snp chips

Selection index

Pull SNP genotype

Selection intensity

Total genetic variance

Phenotypic variance

Make random crosses

Make random crosses

Select and randomly cross

Select families