gl.report.diversity: Calculates diversity indexes for SNPs

Description

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.

Usage

gl.report.diversity(
  x,
  plot.out = TRUE,
  pbar = TRUE,
  table = "DH",
  plot_theme = theme_dartR(),
  plot_colors = discrete_palette,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].

plot.out

Specify if plot is to be produced [default TRUE].

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. [default 'DH'].

plot_theme

Theme for the plot. See Details for options [default theme_dartR()].

plot_colors

A color palette or a list with as many colors as there are populations in the dataset [default discrete_palette].

save2tmp

If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity].

Value

A list of entropy indexes for each level of q and equivalent numbers for alpha and beta diversity.

Details

For all indexes, the entropies (H) and corresponding effective numbers, i.e. Hill numbers (D), which reflect the number of needed entities to get the observed values, are calculated. In a nutshell, the alpha indexes between the different q-values should be similar if there is 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 indexes, we recommend resorting to the literature provided below. Confidence intervals are +/- 1 standard deviation.

Function's output

Plots are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

Examples of other themes that can be used can be consulted in

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

Examples

Run this code

# NOT RUN {
div <- gl.report.diversity(bandicoot.gl, table = FALSE, pbar=FALSE)
div$zero_H_alpha
div$two_H_beta
names(div)

# }

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