Package: AlphaSimR
Type: Package
Title: Breeding Program Simulations
Version: 2.1.0
Date: 2025-11-08
Authors@R: c(person("Chris", "Gaynor", email = "gaynor.robert@hotmail.com",
  role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0558-6656")),
  person("Gregor", "Gorjanc", role = "ctb", 
  comment = c(ORCID = "0000-0001-8008-2787")),
  person("John", "Hickey", role = "ctb", 
  comment = c(ORCID = "0000-0001-5675-3974")),
  person("Daniel", "Money", role = "ctb", 
  comment = c(ORCID = "0000-0001-5151-3648")),
  person("David", "Wilson", role = "ctb"),
  person("Thiago", "Oliveira", role = "ctb",
  comment = c(ORCID = "0000-0002-4555-2584")),
  person("Audrey", "Martin", role = "ctb",
  comment = c(ORCID = "0000-0003-2235-0098")),
  person("Philip", "Greenspoon", role = "ctb",
  comment = c(ORCID = "0000-0001-6284-7248")),
  person("Ros", "Craddock", role = "ctb",
  comment = c(ORCID = "0009-0004-1578-1580")),
  person("Jana", "Obsteter", role = "ctb", 
  comment = c(ORCID = "0000-0003-1511-3916")))
Description: 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>].
License: MIT + file LICENSE
URL: https://github.com/gaynorr/AlphaSimR,
        https://gaynorr.github.io/AlphaSimR/,
        https://www.edx.org/learn/animal-breeding/the-university-of-edinburgh-breeding-programme-modelling-with-alphasimr
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 0.12.7), Rdpack, methods, R6
RdMacros: Rdpack
LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
RoxygenNote: 7.3.3
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Repository: https://gaynorr.r-universe.dev
Date/Publication: 2025-11-24 15:52:35 UTC
RemoteUrl: https://github.com/gaynorr/alphasimr
RemoteRef: HEAD
RemoteSha: 0a60280b8c9c65aaf8afcaee031e3498decd3b21
Packaged: 2026-06-22 09:53:10 UTC; root
Author: Chris Gaynor [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0558-6656>),
  Gregor Gorjanc [ctb] (ORCID: <https://orcid.org/0000-0001-8008-2787>),
  John Hickey [ctb] (ORCID: <https://orcid.org/0000-0001-5675-3974>),
  Daniel Money [ctb] (ORCID: <https://orcid.org/0000-0001-5151-3648>),
  David Wilson [ctb],
  Thiago Oliveira [ctb] (ORCID: <https://orcid.org/0000-0002-4555-2584>),
  Audrey Martin [ctb] (ORCID: <https://orcid.org/0000-0003-2235-0098>),
  Philip Greenspoon [ctb] (ORCID:
    <https://orcid.org/0000-0001-6284-7248>),
  Ros Craddock [ctb] (ORCID: <https://orcid.org/0009-0004-1578-1580>),
  Jana Obsteter [ctb] (ORCID: <https://orcid.org/0000-0003-1511-3916>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>