R/PanbcEstFun.Sam.R

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

PanbcEstFun.Sam <-
function(y1, y2) {
  n1 <- y1[1]
  n2 <- y2[1]
  x1 <- y1[-1]
  x2 <- y2[-1]
  D12 <- sum(x1 > 0 & x2 > 0)
  f11 <- sum(x1 == 1 & x2 == 1)
  f22 <- sum(x1 == 2 & x2 == 2)
  f1p <- sum(x1 == 1 & x2 >= 1)
  fp1 <- sum(x1 >= 1 & x2 == 1)
  f2p <- sum(x1 == 2 & x2 >= 1)
  fp2 <- sum(x1 >= 1 & x2 == 2)
  K1 <- (n1 - 1) / n1
  K2 <- (n2 - 1) / n2
  est <- D12 + K1 * f1p * (f1p - 1) / 2 / (f2p + 1) + 
    K2 * fp1 * (fp1 - 1) / 2 / (fp2 + 1) + 
    K1 * K2 * f11 * (f11 - 1) / 4 / (f22 + 1)
  return(est)
}