calcPheno

internal

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

Ros Craddock

calcPheno function

<dl><dt>pop</dt>
<dd>an object of class Pop</dd>
<dt>varE</dt>
<dd>a vector or matrix of residual variances</dd>
<dt>reps</dt>
<dd>number of reps for phenotype</dd>
<dt>p</dt>
<dd>p-value for environment</dd>
<dt>traits</dt>
<dd>number of traits</dd>
<dt>simParam</dt>
<dd>simulation parameters object</dd></dl>

Arguments

Calculate phenotypes — calcPheno

<dl>

<dt>pop</dt>
<dd>an object of class Pop</dd>


<dt>varE</dt>
<dd>a vector or matrix of residual variances</dd>


<dt>reps</dt>
<dd>number of reps for phenotype</dd>


<dt>p</dt>
<dd>p-value for environment</dd>


<dt>traits</dt>
<dd>number of traits</dd>


<dt>simParam</dt>
<dd>simulation parameters object</dd>

</dl>

Calculate phenotypes

calcPheno: Calculate phenotypes

Description

Usage

Arguments