R/niche.overlap.boot.pair.R

In helixcn/spaa: SPecies Association Analysis

niche.overlap.boot.pair <- function(vectorA, vectorB,
                                    method = c(
                                      "levins", "schoener", "petraitis",
                                      "pianka", "czech", "morisita"
                                    ),
                                    times = 1000, quant = c(0.025, 0.975)) {
  method <- match.arg(method)
  if (!length(vectorA) == length(vectorB)) {
    stop("Length of vectorA differs from lengths of vectorB")
  }
  booted <- rep(NA, times)
  obs <- niche.overlap.pair(vectorA, vectorB, method = method)

  for (i in 1:times) {
    ind <- sample(1:length(vectorA), size = length(vectorA), replace = TRUE)
    booted[i] <- niche.overlap.pair(vectorA[ind], vectorB[ind], method = method)
  }

  result <- c(obs, mean(booted), sd(booted), quantile(booted, quant, na.rm = TRUE), times)
  names(result) <- c("Observed", "Boot mean", "Boot std", "Boot CI1", "Boot CI2", "times")
  return(round(result, 3))
}