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>).

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Description file content

Package
AlphaSimR
Type
Package
Title
Breeding Program Simulations
Version
0.8.2
Date
2018-10-15
Description
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, ).
License
MIT + file LICENSE
URL
Encoding
UTF-8
LazyData
true
Depends
R (>= 3.3.0), methods, R6
Imports
Rcpp (>= 0.12.7)
LinkingTo
Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
RoxygenNote
6.1.0
Suggests
knitr, rmarkdown, testthat
VignetteBuilder
knitr
NeedsCompilation
yes
Packaged
2018-10-15 08:35:02 UTC; rgaynor
Author
Chris Gaynor [aut, cre] (), Gregor Gorjanc [ctb] (), David Wilson [ctb], Daniel Money [ctb], John Hickey [ctb] ()
Maintainer
Chris Gaynor
Repository
CRAN
Date/Publication
2018-10-15 18:20:20 UTC

install.packages('AlphaSimR')

0.8.2

a month ago

https://alphagenes.roslin.ed.ac.uk/wp/software/alphasimr/

Chris Gaynor

MIT + file LICENSE

Depends on

R (>= 3.3.0), methods, R6

Imports

Rcpp (>= 0.12.7)

Suggests

knitr, rmarkdown, testthat

Discussions