gl.sim.offspring

This takes a population (or a single individual) of fathers (provided as a
genlight object) and mother(s) and simulates offspring based on 'random'
 mating. It can be used to simulate population dynamics and check the effect
 of those dynamics and allele frequencies, number of alleles. Another
 application is to simulate relatedness of siblings and compare it to actual
 relatedness found in the population to determine kinship.

Functions are provided that facilitate the import and analysis of
'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data.
The main focus is on data generated by 'DarT' (Diversity Arrays Technology),
however, data from other sequencing platforms can be used once 'SNP' or related
fragment presence/absence data from any source is imported. Genetic datasets
are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility,
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR' supports also the analysis of 3rd party software package
such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version
2.0.3 we also implemented simulation functions, that allow to forward simulate
'SNP' dynamics under different population and evolutionary dynamics.
Comprehensive tutorials and support can be found at our 'github' repository:
github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find
the information by typing citation('dartR') in the console.

Bernd Gruber

dartR

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
Genome-Wide Restriction Fragment Analysis

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

gl.sim.offspring function

<dl><dt>fathers</dt>
<dd>Genlight object of potential fathers [required].</dd>
<dt>mothers</dt>
<dd>Genlight object of potential mothers simulated [required].</dd>
<dt>noffpermother</dt>
<dd>Number of offspring per mother [required].</dd>
<dt>sexratio</dt>
<dd>The sex ratio of simulated offspring 
(females / females +males, 1 equals 100 percent females) [default 0.5.].</dd></dl>

Arguments

Bernd Gruber (Post to <a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Simulates a specified number of offspring based on alleles provided by
 potential father(s) and mother(s) — gl.sim.offspring

<dl>

<dt>fathers</dt>
<dd>Genlight object of potential fathers [required].</dd>


<dt>mothers</dt>
<dd>Genlight object of potential mothers simulated [required].</dd>


<dt>noffpermother</dt>
<dd>Number of offspring per mother [required].</dd>


<dt>sexratio</dt>
<dd>The sex ratio of simulated offspring 
(females / females +males, 1 equals 100 percent females) [default 0.5.].</dd>

</dl>

Bernd Gruber (Post to <a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

gl.sim.offspring: Simulates a specified number of offspring based on alleles provided by potential father(s) and mother(s)

Description

Usage

Value

Arguments

Author

Examples