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. The citation below also includes a link to a 3-minute video that explains, q, D and H.
gl.report.diversity(
x,
plot.display = TRUE,
plot.theme = theme_dartR(),
plot.colors.pop = gl.colors("dis"),
plot.dir = NULL,
plot.file = NULL,
table = "DH",
verbose = NULL
)A list of entropy indexes for each level of q and equivalent numbers for alpha and beta diversity.
Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
Specify if plot is to be displayed in the graphics window [default TRUE].
User specified theme [default theme_dartR()].
A color palette for population plots or a list with as many colors as there are populations in the dataset [default gl.colors("dis")].
Directory to save the plot RDS files [default as specified by the global working directory or tempdir()].
If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
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'].
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].
Bernd Gruber (Post to https://groups.google.com/d/forum/dartr), Contributors: William B. Sherwin, Alexander Sentinella
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. Error bars are +/- 1 standard deviation.
Function's output
If the function's parameter "table" = "DH" (the default value) is used, the output of the function is 20 tables.
The first two show the number of loci used. The name of each of the rest of the tables starts with three terms separated by underscores.
The first term refers to the q value (0 to 2). The q values identify different ways of summarising diversity (H): q=0 is simply the number of alleles per locus, with no information about their relative proportions; q=2 is the expected heterozygosity, ie the chance of drawing two different alleles at random from the population; q=1 is the Shannon measure of ‘surprise, relating to how likely it is that the next allele drawn will be one that has not been seen before (Sherwin et al 2017, 2021, and associated video).
The second term refers to whether it is the diversity measure (H) or its transformation to Hill numbers (D) The D value tells you how many equally-frequent alleles there would need to be to give the corresponding H-value (in the actual population) The D-values are all in units of numbers of alleles, so they can be plotted against the q-value to get a rich representation of the diversity (Box 1, Fig II in Sherwin et al 2017, 2021, and associated video).
The third term refers to whether the diversity is calculated within populations (alpha) or between populations (beta).
In the case of alpha diversity tables, standard deviations have their own table, which finishes with a fourth term: "sd".
In the case of beta diversity tables, standard deviations are in the upper triangle of the matrix and diversity values are in the lower triangle of the matrix.
Plotting
Plot colours can be set with gl.select.colors().
If plot.file is specified, plots are saved to the directory specified by the user, or the global default working directory set by gl.set.wd() or to the tempdir().
Examples of other themes that can be used can be consulted in
Sherwin, W.B., Chao, A., Johst, L., Smouse, P.E. (2017, 2021). Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. TREE 32(12) 948-963. doi:10.1016/j.tree.2017.09.12 AND TREE 36:955-6 doi.org/10.1016/j.tree.2021.07.005 AND 3-Minute video: ars.els-cdn.com/content/image/1-s2.0-S0169534717302550-mmc2.mp4
Other unmatched report:
gl.allele.freq(),
gl.report.basics(),
gl.report.excess.het(),
gl.report.heterozygosity(),
gl.report.polyploid_heterozygosity()
div <- gl.report.diversity(bandicoot.gl, table=FALSE)
div$zero_H_alpha
div$two_H_beta
names(div)
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