.newPop

Creates a new <code>Pop-class</code> from an object of
of the Pop superclass.

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

Philip Greenspoon

.newPop function

<dl><dt>rawPop</dt>
<dd>an object of the pop superclass</dd>
<dt>id</dt>
<dd>optional id for new individuals</dd>
<dt>mother</dt>
<dd>optional id for mothers</dd>
<dt>father</dt>
<dd>optional id for fathers</dd>
<dt>iMother</dt>
<dd>optional internal id for mothers</dd>
<dt>iFather</dt>
<dd>optional internal id for fathers</dd>
<dt>isDH</dt>
<dd>optional indicator for DH/inbred individuals</dd>
<dt>femaleParentPop</dt>
<dd>optional population of female parents</dd>
<dt>maleParentPop</dt>
<dd>optional population of male parents</dd>
<dt>hist</dt>
<dd>optional recombination history</dd>
<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd>
<dt>...</dt>
<dd>additional arguments passed to the finalizePop
function in simParam</dd></dl>

Arguments

Create new population (internal) — .newPop

<dl>

<dt>rawPop</dt>
<dd>an object of the pop superclass</dd>


<dt>id</dt>
<dd>optional id for new individuals</dd>


<dt>mother</dt>
<dd>optional id for mothers</dd>


<dt>father</dt>
<dd>optional id for fathers</dd>


<dt>iMother</dt>
<dd>optional internal id for mothers</dd>


<dt>iFather</dt>
<dd>optional internal id for fathers</dd>


<dt>isDH</dt>
<dd>optional indicator for DH/inbred individuals</dd>


<dt>femaleParentPop</dt>
<dd>optional population of female parents</dd>


<dt>maleParentPop</dt>
<dd>optional population of male parents</dd>


<dt>hist</dt>
<dd>optional recombination history</dd>


<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd>


<dt>...</dt>
<dd>additional arguments passed to the finalizePop
function in simParam</dd>

</dl>

.newPop: Create new population (internal)

Description

Usage

Value

Arguments