R/bitSize.R

In sinnweja/kinship2: Pedigree Functions

# Automatically generated from all.nw using noweb
## renamed from pedBits, part of pedigree.shrink functions

#' Get pedigree bitsize
#'
#' @description
#' Calculate pedigree bitsize, defined as 2 * # NonFounders - # Founders
#'
#' @details
#' This is a utility function used in pedigree.shrink()
#'
#' @param ped A pedigree object
#'
#' @return A list with the following components:
#' \item{bitSize}{ The bitSize of input pedigree }
#' \item{nFounder}{ The number of founders in the pedigree }
#' \item{nNonFounder}{ The number of nonfounders in the pedgiree }
#'
#' @seealso \code{\link{pedigree.shrink}}
#' @export bitSize
bitSize <- function(ped) {
  ## calculate bit size of a pedigree

  if (!("pedigree" %in% class(ped))) {
    stop("Must be a pegigree object.\n")
  }

  father <- ped$findex
  mother <- ped$mindex
  id <- ped$id

  founder <- father == 0 & mother == 0
  pedSize <- length(father)
  nFounder <- sum(founder)
  nNonFounder <- pedSize - nFounder
  bitSize <- 2 * nNonFounder - nFounder
  return(list(
    bitSize = bitSize,
    nFounder = nFounder,
    nNonFounder = nNonFounder
  ))
}