utils.basic.stats

This is a re-implementation of <code>hierfstat::basics.stats</code> specifically 
 for genlight objects. Formula (and hence results) match exactly the original 
version of <code>hierfstat::basics.stats</code> but it is much faster.

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

utils.basic.stats function

<dl><dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd>
<dt>digits</dt>
<dd>Number of decimals to report [default 4]</dd></dl>

Arguments

Luis Mijangos and Carlo Pacioni (bugs? Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
 per locus, per population and various population differentiation measures — utils.basic.stats

<dl>

<dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd>


<dt>digits</dt>
<dd>Number of decimals to report [default 4]</dd>

</dl>

Luis Mijangos and Carlo Pacioni (bugs? Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
 per locus, per population and various population differentiation measures

utils.basic.stats: Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and various population differentiation measures

Description

Usage

Value

Arguments

Author

Examples