R/countKinshipValues.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Counts the number of occurrences of each kinship value seen for a pair of
#' individuals in a series of simulated pedigrees.
#'
#' @return A list of three lists named \code{kIds} (kinship IDs), \code{kValues}
#'         (kinship values), and \code{kCounts} (kinship counts).
#'
#' @param kinshipValues matrix of kinship values from simulated pedigrees where
#'  each row represents a pair of individuals in the pedigree and each column
#'  represents the vector of kinship values generated in a simulated
#'  pedigree.
#' @param accummulatedKValueCounts list object with same structure as that
#'  returned by this function.
#'
#' @export
#' @examples
#'  library(nprcgenekeepr)
#'  ped <- nprcgenekeepr::smallPed
#'  simParent_1 <- list(id = "A",
#'                      sires = c("s1_1", "s1_2", "s1_3"),
#'                      dams = c("d1_1", "d1_2", "d1_3", "d1_4"))
#'  simParent_2 <- list(id = "B",
#'                      sires = c("s1_1", "s1_2", "s1_3"),
#'                      dams = c("d1_1", "d1_2", "d1_3", "d1_4"))
#'  simParent_3 <- list(id = "E",
#'                      sires = c("A", "C", "s1_1"),
#'                      dams = c("d3_1", "B"))
#'  simParent_4 <- list(id = "J",
#'                      sires = c("A", "C", "s1_1"),
#'                      dams = c("d3_1", "B"))
#'  simParent_5 <- list(id = "K",
#'                      sires = c("A", "C", "s1_1"),
#'                      dams = c("d3_1", "B"))
#'  simParent_6 <- list(id = "N",
#'                      sires = c("A", "C", "s1_1"),
#'                      dams = c("d3_1", "B"))
#'  allSimParents <- list(simParent_1, simParent_2, simParent_3,
#'                        simParent_4, simParent_5, simParent_6)
#'
#'  extractKinship <- function(simKinships, id1, id2, simulation) {
#'    ids <- dimnames(simKinships[[simulation]])[[1]]
#'    simKinships[[simulation]][seq_along(ids)[ids == id1],
#'                              seq_along(ids)[ids == id2]]
#'  }
#'
#'  extractKValue <- function(kValue, id1, id2, simulation) {
#'    kValue[kValue$id_1 ==  id1 & kValue$id_2 == id2,
#'           paste0("sim_", simulation)]
#'  }
#'
#'  n <- 10
#'  simKinships <- createSimKinships(ped, allSimParents,
#'                                   pop = ped$id, n = n)
#'  kValues <- kinshipMatricesToKValues(simKinships)
#'  extractKValue(kValues, id1 = "A", id2 = "F", simulation = 1:n)
#'  counts <- countKinshipValues(kValues)
#'  n <- 10
#'  simKinships <- createSimKinships(ped, allSimParents, pop = ped$id, n = n)
#'  kValues <- kinshipMatricesToKValues(simKinships)
#'  extractKValue(kValues, id1 = "A", id2 = "F", simulation = 1:n)
#'  accummulatedCounts <- countKinshipValues(kValues, counts)
countKinshipValues <- function(kinshipValues,
                               accummulatedKValueCounts = NULL) {
  idCols <- c("id_1", "id_2")
  valueCols <- names(kinshipValues)[!is.element(names(kinshipValues), idCols)]
  kIds <- kValues <- kCounts <-
    vector(mode = "list", length = nrow(kinshipValues))

  for (row in seq_len(nrow(kinshipValues))) {
    valuesTable <-
      table(as.numeric(kinshipValues[row, valueCols, with = FALSE]))
    kIds[[row]] <- as.character(kinshipValues[row, idCols, with = FALSE])
    kValues[[row]] <- as.numeric(names(valuesTable))
    kCounts[[row]] <- as.numeric(valuesTable)
  }
  kValueCounts <- list(kIds = kIds,
                       kValues = kValues,
                       kCounts = kCounts)
  if (is.null(accummulatedKValueCounts)) {
    accummulatedKValueCounts <- kValueCounts
  } else {
    if (!all(unique(unlist(kIds)) ==
             unique(unlist(accummulatedKValueCounts$kIds))))
      stop(
        paste0(
          "ID pairs in simulated pedigrees do not match: ",
          setdiff(unique(unlist(kIds)), unique(
            unlist(accummulatedKValueCounts$kIds)
          )),
          " found in only one set of simulated pedigrees."
        )
      )
    for (index in seq_along(kCounts)) {
      valueDiffs <- setdiff(kValues[[index]],
                            accummulatedKValueCounts$kValues[[index]])
      for (value in accummulatedKValueCounts$kValues[[index]]) {
        accummulatedKValueCounts <-
          addKinshipValueCount(accummulatedKValueCounts,
                               kValues,
                               kCounts,
                               index,
                               value)
      }
      if (length(valueDiffs) > 0) {
        accummulatedKValueCounts$kValues[[index]] <-
          c(accummulatedKValueCounts$kValues[[index]], valueDiffs)

        countDiffs <- integer(length(valueDiffs))
        for (value in valueDiffs)
          countDiffs[index] <- kCounts[[index]][kValues[[index]] == value]

        accummulatedKValueCounts$kCounts[[index]] <-
          c(accummulatedKValueCounts$kCounts[[index]], countDiffs)
      }
    }
  }
  accummulatedKValueCounts
}