circle_general: General function for making circular moving window maps
In wingen: Continuous Mapping of Genetic Diversity

circle_general

R Documentation

General function for making circular moving window maps

Description

Generate a continuous raster map using circular moving windows. While resist_gd is built specifically for making maps of genetic diversity from vcfs,circle_general can be used to make maps from different data inputs. Unlike resist_gd, resist_general will not convert your data into the correct format for calculations of different diversity metrics. See details for how to format data inputs for different statistics.

Usage

circle_general(
  x,
  coords,
  lyr,
  maxdist,
  distmat = NULL,
  stat,
  fact = 0,
  rarify = FALSE,
  rarify_n = 2,
  rarify_nit = 5,
  min_n = 2,
  fun = mean,
  L = "nvariants",
  rarify_alleles = TRUE,
  sig = 0.05,
  ...
)

Arguments

`x`	data to be summarized by the moving window (note: order matters! `coords` should be in the same order, there are currently no checks for this). The class of `x` required depends on the statistic being calculated (see the `stat` argument and the function description for more details)
`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)
`maxdist`	maximum geographic distance used to define neighborhood; any samples further than this distance will not be included (this can be thought of as the neighborhood radius) Can either be (1) a single numeric value or (2) a SpatRaster where each pixel is the maximum distance to be used for that cell on the landscape (must be the same spatial scale as `lyr`).
`distmat`	distance matrix output from get_geodist (optional; can be used to save time on distance calculations)
`stat`	moving window statistic to calculate (see details). `stat` can generally be set to any function that will take `x`as input and return a single numeric value (for example, `x` can be a vector and `stat` can be set equal to a summary statistic like `mean`, `sum`, or `sd`)
`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)
`...`	if a function is provided for `stat`, additional arguments to pass to the `stat` function (e.g. if `stat = mean`, users may want to set `na.rm = TRUE`)

Details

To calculate genetic diversity statistics with the built in wingen functions, data must be formatted as such:

for "pi" or "biallelic_richness", x must be a dosage matrix with values of 0, 1, or 2
for "Ho", x must be a heterozygosity matrix where values of 0 = homozygosity and values of 1 = heterozygosity
for "allelic_richness" or ⁠"hwe⁠, x must be a genind type object
for "basic_stats", x must be a hierfstat type object

Otherwise, stat can be any function that takes a matrix or data frame and outputs a single numeric value (e.g., a function that produces a custom diversity index); however, this should be attempted with caution since this functionality has not have been tested extensively and may produce errors.