R/ChaoShared.Sam.R

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

ChaoShared.Sam <-
function(y1, y2, method = c("all","Chao2-shared","Chao2-shared-bc"),conf = 0.95, se = TRUE) {
#function(y1, y2, method = c("all",
#                                              "Chao2-shared",
#                                              "Chao2-shared-bc",
#                                              "Lower-bound",
#                                              "Lower-bound-bc"),
#                           conf = 0.95, se = TRUE) {
  method <- match.arg(method)

  if (method == "all") {
    #a <- Chao2_sharedFun(y1, y2, conf)
    #b <- Chao2_bcFun(y1, y2, conf)
    c <- PanFun.Sam(y1, y2, conf)
    d <- PanbcFun.Sam(y1, y2, conf)
    #out <- rbind(a, b, c, d)
    out <- rbind(c, d)
    rownames(out)<-c("    Chao2-shared","    Chao2-shared-bc")
  }
  #if (method == "Chao2-shared")
  #  out <- Chao2_sharedFun(y1, y2, conf)
  #if (method == "Chao2-shared-bc")
  #  out <- Chao2_bcFun(y1, y2, conf)
  if (method == "Chao2-shared")
    out <- PanFun.Sam(y1, y2, conf)
  if (method == "Chao2-shared-bc")
    out <- PanbcFun.Sam(y1, y2, conf)

  if (se == FALSE) {
    out <- data.frame(Estimator = out[, 1], row.names = rownames(out))
  }
  return(out)
}