R/ChaoShared.Ind.R

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

ChaoShared.Ind <-
function(x1, x2, method = c("all", "Homogeneous",
                              "Heterogeneous(ACE-shared)",
                              "Chao1-shared",
                              "Chao1-shared-bc"),
                              B = 200, conf = 0.95, se = TRUE) {
#function(x1, x2, method = c("all", "Homogeneous",
#                                              "Heterogeneous(ACE-shared)",
#                                              "Chao1(shared)",
#                                              "Chao1-shared-bc",
#                                              "Lower-bound",
#                                              "Lower-bound-bc"),
#                           B = 200, conf = 0.95, se = TRUE) {

  method <- match.arg(method)
  if (se == FALSE)
    B <- 1
  if (method == "all") {
    a <- HomoFun(x1, x2, B, conf)
    b <- HeteroFun(x1, x2, B, conf)
    #c <- Chao1_sharedFun(x1, x2, conf)
    #d <- Chao1_bcFun(x1, x2, conf)
    e <- PanFun(x1, x2, conf)
    f <- PanbcFun(x1, x2, conf)
    #out <- rbind(a, b, c, d, e, f)
    out <- rbind(a, b, e, f)
    rownames(out)<-c("    Homogeneous","    Heterogeneous(ACE-shared)","    Chao1-shared","    Chao1-shared-bc")
  }
  if (method == "Homogeneous")
    out <- HomoFun(x1, x2, B, conf)
  if (method == "Heterogeneous(ACE-shared)")
    out <- HeteroFun(x1, x2, B, conf)
  if (method == "Chao1(shared)")
    out <- Chao1_sharedFun(x1, x2, conf)
  if (method == "Chao1-shared-bc")
    out <- Chao1_bcFun(x1, x2, conf)
  if (method == "Lower-bound")
    out <- PanFun(x1, x2, conf)
  if (method == "Lower-bound-bc")
    out <- PanbcFun(x1, x2, conf)

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