Test multiple K values

Test multiple K values

Usage

tess_ktest(
  gen,
  coords,
  Kvals = 1:10,
  grid = NULL,
  tess_method = "projected.ls",
  lambda = 1,
  K_selection = "manual",
  ploidy = 2,
  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)

Kvals

vector of K values to test

grid

SpatRaster for kriging

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.

K_selection

how to perform K selection ("manual" to enter into console (default) or "auto" for automatic selection based on bestK)

ploidy

ploidy of data (defaults to 2)

quiet

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

Value

list with results from testing different K-values

See also

Other TESS functions: allK_plot_helper(), bestK(), ggbarplot_helper(), krig_legend(), pops_helper(), tess_barplot(), tess_col_default(), tess_do_everything(), tess_ggbarplot(), tess_ggplot(), tess_krig(), tess_plot_allK()