Package: AlphaSimR 1.6.1

Chris Gaynor

AlphaSimR: Breeding Program Simulations

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].

Authors:Chris Gaynor [aut, cre], Gregor Gorjanc [ctb], John Hickey [ctb], Daniel Money [ctb], David Wilson [ctb], Thiago Oliveira [ctb], Audrey Martin [ctb], Philip Greenspoon [ctb]

AlphaSimR_1.6.1.tar.gz
AlphaSimR_1.6.1.tar.gz(r-4.5-noble)AlphaSimR_1.6.1.tar.gz(r-4.4-noble)
AlphaSimR_1.6.1.tgz(r-4.4-emscripten)AlphaSimR_1.6.1.tgz(r-4.3-emscripten)
AlphaSimR.pdf |AlphaSimR.html
AlphaSimR/json (API)
NEWS

# Install 'AlphaSimR' in R:
install.packages('AlphaSimR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/gaynorr/alphasimr/issues

Pkgdown:https://gaynorr.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

7.13 score 2 packages 526 scripts 1.1k downloads 17 mentions 112 exports 6 dependencies

Last updated 1 months agofrom:3c3bfea9dd. Checks:OK: 1 WARNING: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-linux-x86_64WARNINGNov 03 2024

Exports:aaaddSegSiteattritionbvcalcGCAcChrdddoubleGenomeebveditGenomeeditGenomeTopQtlfastRRBLUPgenicVarAgenicVarAAgenicVarDgenicVarGgenParamgetGenMapgetNumThreadsgetPedgetQtlMapgetSnpMapgvhybridCrossimportGenMapimportHaploimportInbredGenoisFemaleisHybridPopisMaleisMapPopisMultiPopisNamedMapPopisPopisRawPopmakeCrossmakeCross2makeDHmeanEBVmeanGmeanPmergeGenomemergePopsmutatenewEmptyPopnewMapPopnewMultiPopnewPopnIndpedigreeCrossphenopopVarpullIbdHaplopullMarkerGenopullMarkerHaplopullQtlGenopullQtlHaplopullSegSiteGenopullSegSiteHaplopullSnpGenopullSnpHaploquickHaplorandCrossrandCross2reduceGenomeresetPopRRBLUPRRBLUP_DRRBLUP_D2RRBLUP_GCARRBLUP_GCA2RRBLUP_SCARRBLUP_SCA2RRBLUP2RRBLUPMemUserunMacsrunMacs2sampleHaploselectCrossselectFamselectIndselectOPselectWithinFamselfselIndexselIntsetEBVsetMarkerHaplosetPhenosetPhenoGCAsetPhenoProgTestSimParamsmithHazelsolveMKMsolveMVMsolveRRBLUPsolveRRBLUP_EMsolveRRBLUP_EM2solveRRBLUP_EM3solveRRBLUPMKsolveRRBLUPMVsolveUVMtransMatusefulnessvarAvarAAvarDvarEBVvarGvarPwritePlinkwriteRecords

Dependencies:BHR6rbibutilsRcppRcppArmadilloRdpack

Introduction to AlphaSimR

Rendered fromintro.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-11-01
Started: 2018-10-12

Traits in AlphaSimR

Rendered fromtraits.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-11-01
Started: 2019-10-11

Readme and manuals

Help Manual

Help pageTopics
Create new population (internal).newPop
Additive-by-additive epistatic deviationsaa
Add segregating site to MapPopaddSegSite
Lose individuals at randomattrition
Breeding valuebv
Calculate GCAcalcGCA
Combine MapPop chromosomescChr
Dominance deviationsdd
Double the ploidy of individualsdoubleGenome
Estimated breeding valueebv
Edit genomeeditGenome
Edit genome - the top QTLeditGenomeTopQtl
Fast RR-BLUPfastRRBLUP
Additive genic variancegenicVarA
Additive-by-additive genic variancegenicVarAA
Dominance genic variancegenicVarD
Total genic variancegenicVarG
Sumarize genetic parametersgenParam
Get genetic mapgetGenMap
Number of available threadsgetNumThreads
Get pedigreegetPed
Get QTL genetic mapgetQtlMap
Get SNP genetic mapgetSnpMap
Genetic valuegv
Hybrid crossinghybridCross
Hybrid populationc,HybridPop-method HybridPop-class isHybridPop [,HybridPop-method
Import genetic mapimportGenMap
Import haplotypesimportHaplo
Import inbred, diploid genotypesimportInbredGeno
Test if individuals of a population are female or maleisFemale isMale
Test if object is of a Population classisPop
Loci metadataLociMap-class
Make designed crossesmakeCross
Make designed crossesmakeCross2
Generates DH linesmakeDH
Raw population with genetic mapc,MapPop-method isMapPop MapPop-class [,MapPop-method
Mean estimated breeding valuesmeanEBV
Mean genetic valuesmeanG
Mean phenotypic valuesmeanP
Combine genomes of individualsmergeGenome
Merge list of populationsmergePops
Multi-Populationc,MultiPop-method isMultiPop length,MultiPop-method MultiPop-class [,MultiPop-method [[,MultiPop-method
Add Random Mutationsmutate
Raw population with genetic map and idc,NamedMapPop-method isNamedMapPop NamedMapPop-class [,NamedMapPop-method
Creates an empty populationnewEmptyPop
New MapPopnewMapPop
Create new Multi PopulationnewMultiPop
Create new populationnewPop
Number of individualsnInd
Pedigree crosspedigreeCross
Phenotypepheno
Populationc,Pop-method length,Pop-method Pop-class show,Pop-method [,Pop-method
Population variancepopVar
Pull IBD haplotypespullIbdHaplo
Pull marker genotypespullMarkerGeno
Pull marker haplotypespullMarkerHaplo
Pull QTL genotypespullQtlGeno
Pull QTL haplotypespullQtlHaplo
Pull segregating site genotypespullSegSiteGeno
Pull seg site haplotypespullSegSiteHaplo
Pull SNP genotypespullSnpGeno
Pull SNP haplotypespullSnpHaplo
Quick founder haplotype simulationquickHaplo
Make random crossesrandCross
Make random crossesrandCross2
Raw Populationc,RawPop-method isRawPop RawPop-class show,RawPop-method [,RawPop-method
Create individuals with reduced ploidyreduceGenome
Reset populationresetPop
RR-BLUP ModelRRBLUP
RR-BLUP Model with DominanceRRBLUP_D
RR-BLUP with Dominance Model 2RRBLUP_D2
RR-BLUP GCA ModelRRBLUP_GCA
RR-BLUP GCA Model 2RRBLUP_GCA2
RR-BLUP SCA ModelRRBLUP_SCA
RR-BLUP SCA Model 2RRBLUP_SCA2
RR-BLUP Model 2RRBLUP2
RRBLUP Memory UsageRRBLUPMemUse
RR-BLUP SolutionRRsol-class
Create founder haplotypes using MaCSrunMacs
Alternative wrapper for MaCSrunMacs2
Sample haplotypes from a MapPopsampleHaplo
Select and randomly crossselectCross
Select familiesselectFam
Select individualsselectInd
Select open pollinating plantsselectOP
Select individuals within familiesselectWithinFam
Self individualsself
Selection indexselIndex
Selection intensityselInt
Set estimated breeding values (EBV)setEBV
Set marker haplotypessetMarkerHaplo
Set phenotypessetPheno
Set GCA as phenotypesetPhenoGCA
Set progeny test as phenotypesetPhenoProgTest
Simulation parametersSimParam
Calculate Smith-Hazel weightssmithHazel
Solve Multikernel ModelsolveMKM
Solve Multivariate ModelsolveMVM
Solve RR-BLUPsolveRRBLUP
Solve RR-BLUP with EMsolveRRBLUP_EM
Solve RR-BLUP with EM and 2 random effectssolveRRBLUP_EM2
Solve RR-BLUP with EM and 3 random effectssolveRRBLUP_EM3
Solve Multikernel RR-BLUPsolveRRBLUPMK
Solve Multivariate RR-BLUPsolveRRBLUPMV
Solve Univariate ModelsolveUVM
Additive traitTraitA-class
Sex specific additive traitTraitA2-class
Sex specific additive and dominance traitTraitA2D-class
Additive and dominance traitTraitAD-class
Additive, dominance, and epistatic traitTraitADE-class
Additive, dominance, epistasis, and GxE traitTraitADEG-class
Additive, dominance and GxE traitTraitADG-class
Additive and epistatic traitTraitAE-class
Additive, epistasis and GxE traitTraitAEG-class
Additive and GxE traitTraitAG-class
Linear transformation matrixtransMat
Usefulness criterionusefulness
Additive variancevarA
Additive-by-additive epistatic variancevarAA
Dominance variancevarD
Variance of estimated breeding valuesvarEBV
Total genetic variancevarG
Phenotypic variancevarP
Writes a Pop-class as PLINK fileswritePlink
Write data recordswriteRecords