randCross2

A wrapper for <code>makeCross2</code> that randomly
selects parental combinations for all possible combinantions between
two populations.

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

randCross2 function

<dl><dt>females</dt>
<dd>an object of <code>Pop-class</code> for female parents.</dd>
<dt>males</dt>
<dd>an object of <code>Pop-class</code> for male parents.</dd>
<dt>nCrosses</dt>
<dd>total number of crosses to make</dd>
<dt>nProgeny</dt>
<dd>number of progeny per cross</dd>
<dt>balance</dt>
<dd>this option will balance the number
of progeny per parent</dd>
<dt>femaleParents</dt>
<dd>an optional vector of indices for allowable
female parents</dd>
<dt>maleParents</dt>
<dd>an optional vector of indices for allowable
male parents</dd>
<dt>ignoreSexes</dt>
<dd>should sex be ignored</dd>
<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd></dl>

Arguments

Make random crosses — randCross2

<dl>

<dt>females</dt>
<dd>an object of <code>Pop-class</code> for female parents.</dd>


<dt>males</dt>
<dd>an object of <code>Pop-class</code> for male parents.</dd>


<dt>nCrosses</dt>
<dd>total number of crosses to make</dd>


<dt>nProgeny</dt>
<dd>number of progeny per cross</dd>


<dt>balance</dt>
<dd>this option will balance the number
of progeny per parent</dd>


<dt>femaleParents</dt>
<dd>an optional vector of indices for allowable
female parents</dd>


<dt>maleParents</dt>
<dd>an optional vector of indices for allowable
male parents</dd>


<dt>ignoreSexes</dt>
<dd>should sex be ignored</dd>


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

</dl>

randCross2: Make random crosses

Description

Usage

Value

Arguments

Examples