wingen function to do everything (preview and generate moving window maps, krige, and mask)

wingen function to do everything (preview and generate moving window maps, krige, and mask)

Usage

wingen_do_everything(
  gen,
  lyr,
  coords,
  wdim = 3,
  fact = 0,
  sample_count = TRUE,
  min_n = 2,
  preview = FALSE,
  stat = "pi",
  rarify = FALSE,
  kriged = FALSE,
  grd = NULL,
  index = 1,
  agg_grd = NULL,
  disagg_grd = NULL,
  agg_r = NULL,
  disagg_r = NULL,
  masked = FALSE,
  mask = NULL,
  bkg = NULL,
  plot_count = FALSE,
  quiet = 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)

lyr

SpatRaster or RasterLayer to slide the window across (see Details for important information about projections). For method = "resist" this should also be the conductivity layer (see resist_gd)

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)

wdim

if method = "window", 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)

sample_count

whether to create plot of sample counts for each cell (defaults to TRUE)

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)

preview

whether to produce preview of raster layer, window and focal cell size using preview_gd (default = FALSE)

stat

genetic diversity statistic(s) to calculate (see Details, defaults to "pi"). Can be a single statistic or a vector of statistics

rarify

if rarify = TRUE, rarefaction is performed (defaults to FALSE)

kriged

whether to smooth out mapped values using kriging using krig_gd (default = FALSE)

grd

object to create grid for kriging; can be a SpatRaster or RasterLayer. If undefined, will use r to create a grid.

index

integer indices of layers in raster stack to krige (defaults to 1; i.e., the first layer)

agg_grd

factor to use for aggregation of grd, if provided (this will decrease the resolution of the final kriged raster; defaults to NULL)

disagg_grd

factor to use for disaggregation of grd, if provided (this will increase the resolution of the final kriged raster; defaults to NULL)

agg_r

factor to use for aggregation of r, if provided (this will decrease the number of points used in the kriging model; defaults to NULL)

disagg_r

factor to use for disaggregation, of r if provided (this will increase the number of points used in the kriging model; defaults to NULL)

masked

whether to mask out areas outside region of interest using mask_gd (default = FALSE)

plot_count

if TRUE, whether to visualize sample counts using plot_count (default = FALSE)

quiet

whether to operate quietly and suppress the output of tables and figures (defaults to FALSE)

Value

RasterBrick object final raster

Details

When using wingen, please cite the original citation: Bishop, A.P., Chambers, E.A., Wang, I.J. (2023). Generating continuous maps of genetic diversity using moving windows. Methods Ecol. Evol. doi: https://doi.org/10.1111/2041-210X.14090 N.B.: Be aware that this function sets many of the wingen function arguments to defaults, which my result in sub optimal results. We highly advise researchers to run each wingen function separately for best results.

See also

Other wingen functions: krig_agg_helper(), krig_helper()