dartR: gl.set.verbosity – R documentation

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gl.set.verbosity

Set the default verbosity level

Description

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 as a flag in the gl@loc.metrics.flags slot of each genelight object. This script sets the value of the flag.

Usage

gl.set.verbosity(x, value = 2, verbose = NULL)

Arguments

`x`	name of the genlight object containing the SNP data, or the genind object containing the SilocoDArT data [required]
`value`	– 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]
`verbose`	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Value

The genlight with the verbosity flag reset

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

gl <- gl.set.verbosity(testset.gl, value=2)

dartR

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

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29