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>].

Version:	1.6.1
Depends:	R (≥ 4.0.0), methods, R6
Imports:	Rcpp (≥ 0.12.7), Rdpack
LinkingTo:	Rcpp, RcppArmadillo (≥ 0.7.500.0.0), BH
Suggests:	knitr, rmarkdown, testthat
Published:	2024-11-01
DOI:	10.32614/CRAN.package.AlphaSimR
Author:	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]
Maintainer:	Chris Gaynor <gaynor.robert at hotmail.com>
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
NeedsCompilation:	yes
Citation:	AlphaSimR citation info
Materials:	README NEWS
In views:	Agriculture
CRAN checks:	AlphaSimR results

Documentation:

Reference manual:	AlphaSimR.pdf
Vignettes:	Introduction (source, R code) Traits (source)

Downloads:

Package source:	AlphaSimR_1.6.1.tar.gz
Windows binaries:	r-devel: AlphaSimR_1.6.1.zip, r-release: AlphaSimR_1.6.1.zip, r-oldrel: AlphaSimR_1.6.1.zip
macOS binaries:	r-release (arm64): AlphaSimR_1.6.1.tgz, r-oldrel (arm64): AlphaSimR_1.6.1.tgz, r-release (x86_64): AlphaSimR_1.6.1.tgz, r-oldrel (x86_64): AlphaSimR_1.6.1.tgz
Old sources:	AlphaSimR archive

Reverse dependencies:

Reverse depends:	evola, SIMplyBee
Reverse suggests:	FieldSimR, hsrecombi

Linking:

Please use the canonical form https://CRAN.R-project.org/package=AlphaSimR to link to this page.