window_gd: Create a moving window map of genetic diversity

In wingen: Continuous Mapping of Genetic Diversity

Create a moving window map of genetic diversity

Description

Generate a continuous raster map of genetic diversity using moving windows.

Usage

window_gd(
  gen,
  coords,
  lyr,
  stat = "pi",
  wdim = 3,
  fact = 0,
  rarify = FALSE,
  rarify_n = NULL,
  rarify_nit = 5,
  min_n = 2,
  fun = mean,
  L = "nvariants",
  rarify_alleles = TRUE,
  sig = 0.05,
  crop_edges = FALSE,
  ...
)

Arguments

gen	genetic data either as an object of type vcf or a path to a vcf file (note: order matters! The coordinate and genetic data should be in the same order; there are currently no checks for this)
coords	coordinates of samples as sf points, a two-column matrix, or a data.frame representing x and y coordinates (see Details for important information about projections)
lyr	SpatRaster or RasterLayer to slide the window across (see Details for important information about projections)
stat	genetic diversity statistic(s) to calculate (see Details, defaults to "pi"). Can be a single statistic or a vector of statistics
wdim	dimensions (height x width) of window; if only one value is provided, a square window is created (defaults to 3 x 3 window)
fact	aggregation factor to apply to lyr (defaults to 0; note: increasing this value reduces computational time)
rarify	if rarify = TRUE, rarefaction is performed (defaults to FALSE)
rarify_n	if rarify = TRUE, number of points to use for rarefaction (defaults to min_n)
rarify_nit	if rarify = TRUE, number of iterations to use for rarefaction (defaults to 5). Can also be set to "all" to use all possible combinations of samples of size rarify_n within the window.
min_n	minimum number of samples to use in calculations (any focal cell with a window containing less than this number of samples will be assigned a value of NA; defaults to 2)
fun	function to use to summarize rarefaction results (defaults to mean, must take na.rm = TRUE as an argument)
L	for calculating "pi", L argument in pi.dosage function. Return the average nucleotide diversity per nucleotide given the length L of the sequence. The wingen default is L = "nvariants", which sets L to the number of variants in the VCF. If L = NULL, returns the sum over SNPs of nucleotide diversity (note: L = NULL is the pi.dosage default which wingen does not use)
rarify_alleles	for calculating "biallelic_richness", whether to perform rarefaction of allele counts as in allelic.richness (defaults to TRUE)
sig	for calculating "hwe", significance threshold (i.e., alpha level) to use for hardy-weinberg equilibrium tests (defaults to 0.05)
crop_edges	whether to remove cells on the edge of the raster where the window is incomplete (defaults to FALSE)
...	deprecated this was intended to be used to pass additional arguments to the stat function, however now formal arguments are used instead (see L, rarify_alleles, and sig). Passing additional arguments using ... is still possible with the ⁠*_general()⁠ functions.

Details

Coordinates and rasters should be in a projected (planar) coordinate system such that raster cells are of equal sizes. Therefore, spherical systems (including latitute-longitude coordinate systems) should be projected prior to use. Transformation can be performed using st_set_crs for coordinates or project for rasters (see vignette for more details).

Current genetic diversity metrics that can be specified with stat include:

• "pi" for nucleotide diversity (default) calculated using hierfstat pi.dosage. Use the L argument to set the sequence length (defaults to dividing by the number of variants).

• "Ho" for average observed heterozygosity across all sites

• "allelic_richness" for average number of alleles across all sites

• "biallelic_richness" for average allelic richness across all sites for a biallelic dataset (this option is faster than "allelic_richness")

• "hwe" for the proportion of sites that are not in Hardy–Weinberg equilibrium, calculated using pegas hw.test at the 0.05 level (other alpha levels can be specified by adding the sig argument; e.g., sig = 0.10).

• "basic_stats" for a series of statistics produced by hierfstat basic.stats including mean observed heterozygosity (same as Ho), mean gene diversities within population (Hs), Gene diversities overall (Ht), and Fis following Nei (1987). Population-based statistics (e.g., FST) normally reported by basic.stats are not included as they are not meaningful within the individual-based moving windows.

Value

SpatRaster that includes raster layers of genetic diversity and a raster layer of the number of samples within the window for each cell

Examples

load_mini_ex()
wpi <- window_gd(mini_vcf, mini_coords, mini_lyr, rarify = TRUE)

wingen documentation built on May 29, 2024, 9:59 a.m.