Pop-class

[,Pop-method

c,Pop-method

show,Pop-method

Extends <code>RawPop-class</code> to add sex, 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

John Hickey

Daniel Money

David Wilson

Thiago Oliveira

Audrey Martin

Pop-class function

<dl><dt>x</dt>
<dd>a 'Pop' object</dd>
<dt>i</dt>
<dd>index of individuals</dd>
<dt>...</dt>
<dd>additional 'Pop' objects</dd>
<dt>object</dt>
<dd>a 'Pop' object</dd></dl>

Arguments

<ul>
<li><code>[</code>: Extract Pop by index or id</li>
<li><code>c(Pop)</code>: Combine multiple Pops</li>
<li><code>show(Pop)</code>: Show population summary</li>
</ul>

Methods (by generic)

<dl>
<dt><code>id</code></dt>
<dd>an individual's identifier</dd></dl>
<dt><code>iid</code></dt>
<dd>an individual's internal identifier</dd>
<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>sex</code></dt>
<dd>sex of individuals: "M" for males, "F" for females,
and "H" for hermaphrodites</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 p=0.5. 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>misc</code></dt>
<dd>a list whose elements correspond to individuals in the
population. This list is normally empty and exists solely as an
open slot available for uses to store extra information about
individuals.</dd>

Slots

Population — Pop-class

<dl>

<dt>x</dt>
<dd>a 'Pop' object</dd>


<dt>i</dt>
<dd>index of individuals</dd>


<dt>...</dt>
<dd>additional 'Pop' objects</dd>


<dt>object</dt>
<dd>a 'Pop' object</dd>

</dl>

<dl>
<dt><code>id</code></dt>
<dd>an individual's identifier</dd>


<dt><code>iid</code></dt>
<dd>an individual's internal identifier</dd>


<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>sex</code></dt>
<dd>sex of individuals: "M" for males, "F" for females,
and "H" for hermaphrodites</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 p=0.5. 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>misc</code></dt>
<dd>a list whose elements correspond to individuals in the
population. This list is normally empty and exists solely as an
open slot available for uses to store extra information about
individuals.</dd>


</dl>

Pop-class: Population

Description

Usage

Arguments

Methods (by generic)

Slots