Pop-class

[,Pop-method

c,Pop-method

Extends <code><a rd-options="" href="/link/RawPop-class?package=AlphaSimR&version=0.10.0" data-mini-rdoc="AlphaSimR::RawPop-class">RawPop-class</a></code> to add gender, genetic values, 
phenotypes, and pedigrees.

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>].

Chris Gaynor

AlphaSimR

Breeding Program Simulations

Gregor Gorjanc

David Wilson

Daniel Money

John Hickey

Pop-class function

<ul>
<li><code>[</code>: Extract Pop by index or id</li>
<li><code>c</code>: Combine multiple Pops</li>
</ul>

Methods (by generic)

<dl class="dl-horizontal">
<dt><code>id</code></dt><dd>an individual's identifier</dd></dl><dt><code>mother</code></dt><dd>the identifier of the individual's mother</dd><dt><code>father</code></dt><dd>the identifier of the individual's father</dd><dt><code>gender</code></dt><dd>gender of individuals</dd><dt><code>nTraits</code></dt><dd>number of traits</dd><dt><code>gv</code></dt><dd>matrix of genetic values. When using GxE traits,
gv reflects gv when w=0. Dimensions are nInd by nTraits.</dd><dt><code>pheno</code></dt><dd>matrix of phenotypic values. Dimensions are
nInd by nTraits.</dd><dt><code>ebv</code></dt><dd>matrix of estimated breeding values. Dimensions 
are nInd rows and a variable number of columns.</dd><dt><code>gxe</code></dt><dd>list containing GxE slopes for GxE traits</dd><dt><code>fixEff</code></dt><dd>a fixed effect relating to the phenotype. 
Used by genomic selection models but otherwise ignored.</dd><dt><code>reps</code></dt><dd>the number of replications used to measure the 
phenotype. Used by genomic selection models, but otherwise ignored.</dd>

Slots

Extends <code><a rd-options='' href='RawPop-class'>RawPop-class</a></code> to add gender, genetic values, 
phenotypes, and pedigrees.

Pop-class: Population

Description

Usage

Arguments

Methods (by generic)

Slots