dartR.base (version 1.0.5)

gl.report.allelerich: 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
)

Value

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

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].

Author

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

Details

details

• raw allele count

• allelic richness

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)