SimParam

Container for global simulation parameters. Saving this object 
as SP will allow it to be accessed by function defaults.

datasets

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

SimParam function

An object of class <code>R6ClassGenerator</code> of length 24.

Format

<dl class="dl-horizontal">
<dt><code>ploidy</code></dt><dd>ploidy level of species</dd></dl><dt><code>nChr</code></dt><dd>number of chromosomes</dd><dt><code>nTraits</code></dt><dd>number of traits</dd><dt><code>nSnpChips</code></dt><dd>number of SNP chips</dd><dt><code>segSites</code></dt><dd>segregating sites per chromosome</dd><dt><code>gender</code></dt><dd>is gender used for mating</dd><dt><code>genMap</code></dt><dd>"matrix" of chromsome genetic maps</dd><dt><code>femaleMap</code></dt><dd>"matrix" of chromsome genetic maps for 
females</dd><dt><code>maleMap</code></dt><dd>"matrix" of chromsome genetic maps for 
males</dd><dt><code>sepMap</code></dt><dd>are there seperate genetic maps for 
males and females</dd><dt><code>recombRatio</code></dt><dd>ratio of genetic recombination in 
females relative to male</dd><dt><code>traits</code></dt><dd>list of trait</dd><dt><code>snpChips</code></dt><dd>list of SNP chips</dd><dt><code>potQtl</code></dt><dd>list of potential QTL segregating sites</dd><dt><code>potSnp</code></dt><dd>list of potential SNP segregating sites</dd><dt><code>lastId</code></dt><dd>last ID number assigned</dd><dt><code>isTrackPed</code></dt><dd>is pedigree being tracked</dd><dt><code>pedigree</code></dt><dd>pedigree matrix for all individuals</dd><dt><code>isTrackRec</code></dt><dd>is recombination being tracked</dd><dt><code>recHist</code></dt><dd>list of historic recombination events</dd><dt><code>varA</code></dt><dd>additive genetic variance in founderPop</dd><dt><code>varG</code></dt><dd>total genetic variance in founderPop</dd><dt><code>varE</code></dt><dd>default error variance</dd><dt><code>founderPop</code></dt><dd>the founder population used for scaling traits</dd><dt><code>nThreads</code></dt><dd>number of threads used on platforms with OpenMP support</dd>

SimParam: Simulation parameters

Description

Usage

Arguments

Format

Fields