sampleHaplo

Creates a new <code>MapPop-class</code> from an existing
<code>MapPop-class</code> by randomly sampling haplotypes.

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

sampleHaplo function

<dl><dt>mapPop</dt>
<dd>the <code>MapPop-class</code> used to
sample haplotypes</dd>
<dt>nInd</dt>
<dd>the number of individuals to create</dd>
<dt>inbred</dt>
<dd>should new individuals be fully inbred</dd>
<dt>ploidy</dt>
<dd>new ploidy level for organism. If NULL,
the ploidy level of the mapPop is used.</dd>
<dt>replace</dt>
<dd>should haplotypes be sampled with replacement</dd></dl>

Arguments

Sample haplotypes from a MapPop — sampleHaplo

<dl>

<dt>mapPop</dt>
<dd>the <code>MapPop-class</code> used to
sample haplotypes</dd>


<dt>nInd</dt>
<dd>the number of individuals to create</dd>


<dt>inbred</dt>
<dd>should new individuals be fully inbred</dd>


<dt>ploidy</dt>
<dd>new ploidy level for organism. If NULL,
the ploidy level of the mapPop is used.</dd>


<dt>replace</dt>
<dd>should haplotypes be sampled with replacement</dd>

</dl>

sampleHaplo: Sample haplotypes from a MapPop

Description

Usage

Value

Arguments

Examples