utils.collapse.matrix

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Facilitates 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.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
supports the installation of all packages in the 'dartRverse'.
If you want to cite 'dartR', you find the information by typing citation('dartR.base')
in the console.

Bernd Gruber

dartR.base

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

Ching Ching Lau

utils.collapse.matrix function

<dl><dt>D</dt>
<dd>Name of the matrix containing the distances between individuals [required].</dd>
<dt>x</dt>
<dd>Name of the genlight object containing the genotypes [required].</dd>
<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
 progress log; 3, progress and results summary; 5, full report [default 2]. 
@details
This script takes a matrix of distances calculated between individuals and collapses it by averaging to a matrix of distances between populations.
The script gl.dist.ind has a lot of options for distances for presence absence data, but gl.dist.pop does not. This script allows efficient and
consistent transfer of this capability to gl.dist.pop.</dd></dl>

Arguments

Author: Arthur Georges. Custodian: Arthur Georges -- Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>

Author

Collapses a distance matrix calculated for individuals to a distance matrix for populations defined in a dartR
genlight object — utils.collapse.matrix

<dl>

<dt>D</dt>
<dd>Name of the matrix containing the distances between individuals [required].</dd>


<dt>x</dt>
<dd>Name of the genlight object containing the genotypes [required].</dd>


<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
 progress log; 3, progress and results summary; 5, full report [default 2]. 
@details
This script takes a matrix of distances calculated between individuals and collapses it by averaging to a matrix of distances between populations.
The script gl.dist.ind has a lot of options for distances for presence absence data, but gl.dist.pop does not. This script allows efficient and
consistent transfer of this capability to gl.dist.pop.</dd>

</dl>

Author: Arthur Georges. Custodian: Arthur Georges -- Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>

utils.collapse.matrix: Collapses a distance matrix calculated for individuals to a distance matrix for populations defined in a dartR genlight object

Description

Usage

Value

Arguments

Author

See Also