Breeding Program Simulations

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) ]. 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) ].

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'.


Changes in version 0.9.0

New features -added support for autopolyploids -added RRBLUP_GCA2 -randCross2 can now "balance" crossing when not using gender

Bug fixes -fixed recombination tracking bug in createDH2 -removed bug in setEBV with append=TRUE

Changes in version 0.8.2

Bug fixes -fixed ambiguous overloading in optimize.cpp

Changes in version 0.8.1

Bug fixes -setPheno (not setPhenoGCA) passes the number of reps to populations -fixed bug in editGenomeTopQtl -fixed bug in RRBLUP_D -fixed bug in resetPop -fixed bug in SimParam_rescaleTraits -removed unimplemented SimParam_restrSnpSites and SimParam_restrQtlSites -add error message for no traits in calcGCA

Changes in version 0.8.0

New features -added GxE traits with zero environmental variance -faster trait scaling -faster calculation of genetic values -dsyevr now called via arma_fortran -added OpenMP support -parallelized cross2 -parallelized runMacs -parallelized calculation of genetic values -variance calculations now account for inbreeding

Bug fixes -fixes for male selection in selectOP

Changes in version 0.7.1

Bug fixes -add fixEff to setPhenoGCA

Changes in version 0.7.0

New features -added default runMacs option to return all segSites -added ability to specify seperate male and female genetic maps -pullGeno and pullHaplo functions can now specifiy chromosomes -added RRBLUP2 for special GS cases -improved speed by replacing Rcpp random number generators -changed available MaCS species -$MAJOR CHANGE$ GS functions now use populations directly -added pullIbdHaplo -added writePlink

Bug fixes -fixed population subsetting checks to prevent invalid selections -fixed slow calcGCA -fixed error in addTraitAG preventing multiple traits -fixed bug with mergePops when merging ebv -fixed bug in setVarE when using H2 and multiple traits

Changes in version 0.6.1

New features -selectFam now handles half-sib families -selectWithinFam now handles half-sib families

Bug fixes -Removed restriction on varE=NULL in setPhenoGCA

Changes in version 0.6.0

New features -Added NEWS file -Added selectOP to model selection in open pollinating plants -Added runMacs2 as a wrapper for runMacs

Bug fixes -Fixed error when using H2 in SimParam_setVarE

Reference manual

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1.0.4 by Chris Gaynor, 4 months ago

Browse source code at

Authors: Chris Gaynor [aut, cre] , Gregor Gorjanc [ctb] , John Hickey [ctb] , Daniel Money [ctb] , David Wilson [ctb]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports Rcpp

Depends on methods, R6

Suggests knitr, rmarkdown, testthat

Linking to Rcpp, RcppArmadillo, BH

Suggested by hsrecombi.

See at CRAN