gl.report.allelerich: Report allelic richness per population from a genlight object

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Report allelic richness per population from a genlight object

Description

This function needs package adegenet, please install it.

Usage

gl.report.allelerich(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.dir = NULL,
  plot.file = NULL,
  error.bar = "SD",
  verbose = 2
)

Arguments

x	A genlight file (works only for diploid data) [required].
plot.display	Specify if plot is to be produced [default TRUE].
plot.theme	Theme for the plot. See Details for options [default theme_dartR()].
plot.dir	Directory to save the plot RDS files [default as specified by the global working directory or tempdir()].
plot.file	Name for the RDS binary file to save (base name only, exclude extension) [default NULL].
error.bar	Statistic to be plotted as error bar either "SD" (standard deviation) or "SE" (standard error) or "CI" (confidence intervals) [default "SD"].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

details

• raw allele count

• allelic richness

Value

A dataframe containing richness per site, richness per population, raw reference allele count, raw alternate allele count.

Author(s)

Ching Ching Lau (Post to https://groups.google.com/d/forum/dartr)

References

• El Mousadik, A., & Petit, R. J. (1996). High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and applied genetics, 92, 832-839.

Examples

 gl.report.allelerich(possums.gl)

dartR.base documentation built on April 4, 2025, 2:45 a.m.