gl.set.verbosity

dartR functions have a verbosity parameter that sets the level of reporting
 during the execution of the function. The verbosity level, set by parameter
 'verbose' can be one of verbose 0, silent or fatal errors; 1, begin and end;
 2, progress log; 3, progress and results summary; 5, full report. The
 default value for verbosity is stored in the r environment. This script sets
 the default value.

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

gl.set.verbosity function

<dl><dt>value</dt>
<dd>Set the default verbosity to be this value: 0, silent only fatal
errors; 1, begin and end; 2, progress log; 3, progress and results summary;
5, full report [default 2]</dd></dl>

Arguments

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

Author

Sets the default verbosity level — gl.set.verbosity

<dl>

<dt>value</dt>
<dd>Set the default verbosity to be this value: 0, silent only fatal
errors; 1, begin and end; 2, progress log; 3, progress and results summary;
5, full report [default 2]</dd>

</dl>

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

gl.set.verbosity: Sets the default verbosity level

Description

Usage

Value

Arguments

Author

Examples