TESS function to do everything

Usage

tess_do_everything(
  gen,
  coords,
  grid = NULL,
  Kvals = 1:10,
  K_selection = "manual",
  plot_method = "maxQ",
  col_breaks = 20,
  minQ = 0.1,
  tess_method = "projected.ls",
  lambda = 1,
  ploidy = 2,
  correct_kriged_Q = TRUE,
  quiet = FALSE
)

Arguments

gen: genotype dosage matrix (rows = individuals & columns = snps) or vcfR object
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)
grid: SpatRaster for kriging
Kvals: vector of K values to test
K_selection: how to perform K selection ("manual" to enter into console (default) or "auto" for automatic selection based on bestK)
plot_method: method for making rainbow map of kriged layers (options: "maxQ" to only plot the max Q value for each cell (default), "allQ" to plot all Q values greater than minQ, "maxQ_poly" or "allQ_poly" to create the plots as previously described, but as polygons for each K instead of continuous Q values)
col_breaks: number of breaks for plotting (defaults to 20)
minQ: threshold for minimum Q value for rainbow plotting if method = "all" is used (defaults to 0.10)
tess_method: the type of TESS method to be run ("projected.ls" for projected least squares algorithm (default) or "qp" for quadratic programming algorithm)
lambda: numeric value for the spatial regularization parameter. The default value lambda = 1 attributes equal weights to the loss function and to the penalty function.
ploidy: ploidy of data (defaults to 2)
correct_kriged_Q: whether to correct kriged Q values so values greater than 1 are set to 1 and values less than 0 are set to 0 (defaults to TRUE)
quiet: whether to operate quietly and suppress the output of tables and figures (defaults to FALSE)

Value

list with all TESS results, final K value, and final kriged raster

Details

TESS is run using the tess3r package: Caye, K., François, O. (2016). tess3r: Inference of Spatial Population Genetic Structure. R package version 1.1.0. See also: Caye, K., Deist, T.M., Martins, H., Michel, O., François, O. (2016). TESS3: fast inference of spatial population structure and genome scans for selection. Mol. Ecol. Res. 16(2):540-548. https://doi.org/10.1111/1755-0998.12471

Coordinates and rasters should be in a projected (planar) coordinate system. 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).