R/SpecAbunOut.R

In AnneChao/SpadeR: Species-Richness Prediction and Diversity Estimation with R

SpecAbunOut <-
function(data,
                       method = c("all", "Homogeneous", "Chao", "CE", "Jackknife"),
                       k, conf){
  data <- as.numeric(data)
  method <- match.arg(method)
  if (method == "all") {
    a <- SpecAbunHomo(data, k, conf)
    b <- SpecAbunHomoMle(data, k, conf)
    c <- SpecAbunChao1(data, k, conf)
    d <- SpecAbunChao1bc(data, k, conf)
    e <- SpecAbuniChao1(data, k, conf)
    f <- SpecAbunAce(data, k, conf)
    g <- SpecAbunAce1(data, k, conf)
    h <- SpecAbunJack1(data, k, conf)
    i <- SpecAbunJack2(data, k, conf)
    out <- rbind(a, b, c, d, e, f, g, h, i)
	rownames(out) <- c("    Homogeneous Model",
						"    Homogeneous (MLE)",
						"    Chao1 (Chao, 1984)",
						"    Chao1-bc",
						"    iChao1 (Chiu et al. 2014)",
						"    ACE (Chao & Lee, 1992)",
						"    ACE-1 (Chao & Lee, 1992)",
						"    1st order jackknife",
						"    2nd order jackknife")
  }

  if (method == "Homogeneous")
    out <- rbind(SpecAbunHomo(data, k, conf), SpecAbunHomoMle(data, k, conf))
  if (method == "Chao")
    out <- rbind(SpecAbunChao1(data, k, conf), SpecAbunChao1bc(data, k, conf), SpecAbuniChao1(data, k, conf))
  if (method == "CE")
    out <- rbind(SpecAbunAce(data, k, conf), SpecAbunAce1(data, k, conf))
  if (method == "Jackknife")
    out <- rbind(SpecAbunJack1(data, k, conf), SpecAbunJack2(data, k, conf))
  colnames(out) <- c("Estimate", "s.e.", paste(conf*100,"%Lower",sep=""), paste(conf*100,"%Upper",sep=""))
  return(out)
}