Take a pedigree and turn it into an extended environmental relatedness matrix

Usage

ped2ce(
  ped,
  personID = "ID",
  keep_ids = NULL,
  sparse = FALSE,
  verbose = FALSE,
  ...
)

Arguments

ped: a pedigree dataset. Needs ID, momID, and dadID columns
personID: Character. Column name for individual IDs.
keep_ids: character vector of IDs to retain in the final relatedness matrix. When supplied, only the rows of r2 corresponding to these IDs are used in the tcrossprod, so the result is a length(keep_ids) x length(keep_ids) matrix. All columns of r2 are retained during the multiplication so relatedness values remain correct. IDs not found in the pedigree are silently dropped with a warning.
sparse: logical. If TRUE, use and return sparse matrices from Matrix package
verbose: logical. If TRUE, print progress through stages of algorithm
...: additional arguments to be passed to ped2com

Details

The algorithms and methodologies used in this function are further discussed and exemplified in the vignette titled "examplePedigreeFunctions". For more advanced scenarios and detailed explanations, consult this vignette.