ourMELONS/R/newGetDistances.R

newGetDistances <- function(data, rowsFromInd) {
  ninds <- base::max(data[, ncol(data)])
  nloci <- size(data, 2) - 1
  riviLkm <- choose(ninds, 2)

  empties <- matlab2r::find(data < 0)
  data[empties] <- 0
  data <- apply(data, 2, as.numeric) # base::max(noalle) oltava <256

  pariTaulu <- zeros(riviLkm, 2)
  aPointer <- 1
  for (a in 1:(ninds - 1)) {
    pariTaulu_rows <- aPointer:(aPointer + ninds - 1 - a)
    pariTaulu[pariTaulu_rows, 1] <- ones(ninds - a, 1) * a
    pariTaulu[pariTaulu_rows, 2] <- t((a + 1):ninds)
    aPointer <- aPointer + ninds - a
  }

  eka <- pariTaulu[, ones(1, rowsFromInd)]
  eka <- eka * rowsFromInd
  miinus <- repmat((rowsFromInd - 1):0, c(riviLkm, 1))
  eka <- eka - miinus

  toka <- pariTaulu[, ones(1, rowsFromInd) * 2]
  toka <- toka * rowsFromInd
  toka <- toka - miinus

  summa <- zeros(riviLkm, 1)
  vertailuja <- zeros(riviLkm, 1)

  rm(pariTaulu, miinus)

  x <- zeros(size(eka))
  x <- apply(x, 2, as.integer)
  y <- zeros(size(toka))
  y <- apply(y, 2, as.integer)

  for (j in seq_len(nloci)) {
    for (k in 1:rowsFromInd) {
      x[, k] <- data[eka[, k], j]
      y[, k] <- data[toka[, k], j]
    }
    for (a in 1:rowsFromInd) {
      for (b in 1:rowsFromInd) {
        vertailutNyt <- as.double(x[, a] > 0 & y[, b] > 0)
        vertailuja <- vertailuja + vertailutNyt
        lisays <- (x[, a] != y[, b] & vertailutNyt)
        summa <- summa + as.double(lisays)
      }
    }
  }

  rm(x, y, vertailutNyt)
  nollat <- matlab2r::find(vertailuja == 0)
  dist <- zeros(length(vertailuja), 1)
  dist[nollat] <- 1
  muut <- matlab2r::find(vertailuja > 0)
  dist[muut] <- summa[muut] / vertailuja[muut]
  rm(summa, vertailuja)
  Z <- linkage(t(dist))
  return(list(Z = Z, dist = dist))
}