ourMELONS/R/computePopulationLogml.R

computePopulationLogml <- function(pops, adjprior, priorTerm) {
  # Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset

  # ======================================================== #
  # Limiting COUNTS size                                     #
  # ======================================================== #
  COUNTS <- COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop = FALSE]

  x <- size(COUNTS, 1)
  y <- size(COUNTS, 2)
  z <- length(pops)

  # ======================================================== #
  # Computation                                              #
  # ======================================================== #
  isarray <- length(dim(repmat(adjprior, c(1, 1, length(pops))))) > 2
  # FIXME: 3rd dimension of COUNTS getting dropped
  term1 <- squeeze(
    sum(
      sum(
        reshape(
          lgamma(
            repmat(adjprior, c(1, 1, length(pops))) +
              COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop = !isarray]
          ),
          c(x, y, z)
        ),
        1
      ),
      2
    )
  )
  if (is.null(priorTerm)) priorTerm <- 0
  popLogml <- term1 - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
  return(popLogml)
}