R/niche.overlap.pair.R

In helixcn/spaa: SPecies Association Analysis

niche.overlap.pair <-
  function(vectA, vectB, method = c("pianka", "schoener", "petraitis", "czech", "morisita", "levins")) {
    method <- match.arg(method)
    nij <- vectA
    pij <- nij / sum(nij)

    nkj <- vectB
    pkj <- nkj / sum(nkj)
    switch(method,
      levins = {
        upper <- sum(pij * pkj)
        lower <- sum(pij^2)
        result <- upper / lower
      },
      schoener = {
        result <- 1 - sum(abs(pij - pkj)) / 2
      },
      petraitis = {
        nij <- nij[(vectA > 0) & (vectB > 0)]
        pij <- nij / sum(nij)
        nkj <- nkj[(vectA > 0) & (vectB > 0)]
        pkj <- nkj / sum(nkj)
        Eik <- sum(pij * log(pkj)) - sum(pij * log(pij))
        result <- exp(Eik)
      },
      pianka = {
        result <- sum(pij * pkj) / sqrt((sum(pij^2)) * (sum(pkj^2)))
      },
      czech = {
        result <- 1 - (sum(abs(pij - pkj))) / 2
      },
      morisita = {
        result <- 2 * sum(pij * pkj) / ((sum(pij^2)) + (sum(pkj^2)))
      }
    )
    return(result)
  }