dartR: gl.report.diversity – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

gl.report.diversity

Calculate diversity indices for SNPs

Description

!!Just an intro placeholder!! This script takes a genlight object and calculates alpha and beta diversity for q=0:2. Formulas are taken from Sherwin et al. 2017. The paper describes nicely the relationship between the different q levels and how they relate to population genetic processes such as dispersal and selection. For all indices the entropies (H) and corrosponding effective numbers Hill numbers (D), which reflect the amount of entities that are needed to get the observed valuea are calculated. In a nutshell the alpha indices between the different q-values should be similar if there are no deviation from expected allele frequencies and occurrences (e.g. all loci in HWE & equilibrium). If there is a deviation of an index this links to a process causing it such as dispersal, selection or strong drift. For a detailed explanation of all the indices, we recommend to resort to the literature provided below.

Usage

gl.report.diversity(
  gl,
  spectrumplot = TRUE,
  confiplot = FALSE,
  pbar = TRUE,
  table = "DH",
  verbose = NULL
)

Arguments

`gl`	genlight object containing the SNP genotypes [required]
`spectrumplot`	switch to provide a plot [default TRUE]
`confiplot`	switch if confidence intervals (1 sd) should be drawn [default FALSE]
`pbar`	report on progress. Silent if set to FALSE. [default TRUE]
`table`	prints a tabular output to the console either 'D'=D values, or 'H'=H values or 'DH','HD'=both or 'N'=no table.
`verbose`	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

returns a list of entropy indices for each level of q and equivalent numbers for alpha and beta diversity.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr), Contributors: William B. Sherwin, Alexander Sentinella

References

Sherwin, W.B., Chao, A., Johst, L., Smouse, P.E. (2017). Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. TREE 32(12) 948-963. doi:10.1016/j.tree.2017.09.12

Chao et al. 2014

Examples

div <- gl.report.diversity(bandicoot.gl, spectrumplot = TRUE, table = FALSE, pbar=FALSE)
div$zero_H_alpha
div$two_H_beta
names(div)

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