R/niche.overlap.R

In helixcn/spaa: SPecies Association Analysis

niche.overlap <-
  function(mat, method = c(
             "levins", "schoener", "petraitis",
             "pianka", "czech", "morisita"
           )) {
    match.arg(method)
    mat <- na.omit(mat)
    result <- rep(NA, ncol(mat) * ncol(mat))
    dim(result) <- c(ncol(mat), ncol(mat))
    rownames(result) <- colnames(mat)
    colnames(result) <- colnames(mat)
    for (i in 1:(ncol(mat) - 1)) {
      for (j in (i + 1):ncol(mat)) {
        if (method == "levins") {
          result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
            method = "levins"
          )
        } else {
          if (method == "schoener") {
            result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
              method = "schoener"
            )
          } else {
            if (method == "petraitis") {
              result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
                method = "petraitis"
              )
            } else {
              if (method == "pianka") {
                result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
                  method = "pianka"
                )
              } else {
                if (method == "czech") {
                  result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
                    method = "czech"
                  )
                } else {
                  if (method == "morisita") {
                    result[j, i] <- niche.overlap.pair(mat[, i], mat[, j],
                      method = "morisita"
                    )
                  }
                }
              }
            }
          }
        }
      }
    }
    return(as.dist(result))
  }