# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "AlphaSimR" in publications use:'
type: software
license: MIT
title: 'AlphaSimR: Breeding Program Simulations'
version: 2.1.0
doi: 10.1093/g3journal/jkaa017
identifiers:
- type: doi
  value: 10.32614/CRAN.package.AlphaSimR
- type: url
  value: https://www.edx.org/learn/animal-breeding/the-university-of-edinburgh-breeding-programme-modelling-with-alphasimr
abstract: The successor to the 'AlphaSim' software for breeding program simulation
  [Faux et al. (2016) <https://doi.org/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) <https://doi.org/10.1101/gr.083634.108>].
authors:
- family-names: Gaynor
  given-names: Chris
  email: gaynor.robert@hotmail.com
  orcid: https://orcid.org/0000-0003-0558-6656
preferred-citation:
  type: article
  title: 'AlphaSimR: an R package for breeding program simulations'
  authors:
  - family-names: Gaynor
    given-names: R Chris
  - family-names: Gorjanc
    given-names: Gregor
  - family-names: Hickey
    given-names: John M
  journal: G3 Gene|Genomes|Genetics
  year: '2021'
  volume: '11'
  issue: jkaa07
  url: https://doi.org/10.1093/g3journal/jkaa017
  doi: 10.1093/g3journal/jkaa017
repository: https://highlanderlab.r-universe.dev
repository-code: https://github.com/gaynorr/AlphaSimR
commit: 0a60280b8c9c65aaf8afcaee031e3498decd3b21
url: https://gaynorr.github.io/AlphaSimR/
date-released: '2025-11-08'
contact:
- family-names: Gaynor
  given-names: Chris
  email: gaynor.robert@hotmail.com
  orcid: https://orcid.org/0000-0003-0558-6656
references:
- type: article
  title: Plant breeding simulations with AlphaSimR
  authors:
  - family-names: Bančič
    given-names: Jon
  - family-names: Greenspoon
    given-names: Philip
  - family-names: Gaynor
    given-names: R Chris
  - family-names: Gorjanc
    given-names: Gregor
  journal: Crop Science
  year: '2025'
  volume: '65'
  issue: e21312
  url: https://doi.org/10.1002/csc2.21312
  doi: 10.1002/csc2.21312