R/SpecInciModelth.R

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

SpecInciModelth <-
function(data, k, conf){
  data <- as.numeric(data)
  z <- -qnorm((1 - conf)/2)
  t <- length(data[1, ])
  dat <- apply(data, 1, sum) 
  
  x <- dat[which(dat != 0)]
  Q <- function(i, data){length(data[which(data == i)])}
  
  basicInci <- function(data, k){
    data <- as.numeric(data)
    t <- data[1]
    dat <- data[-1]
    x <- dat[which(dat != 0)]
    Q <- function(i, data){length(data[which(data == i)])}
    
    D <- length(x)
    D_infreq <- length(x[which(x <= k)])
    
    if (Q(1, x) > 0 & Q(2, x) > 0){
      A <- 2*Q(2, x)/((t-1)*Q(1, x) + 2*Q(2, x))
    } else if (Q(1, x) > 0 & Q(2, x) == 0){
      A <- 2/((t-1)*(Q(1, x) - 1) + 2)
    } else {
      A <- 1
    }
    C_infreq <- 1 - Q(1, x)/sum(x[which(x <= k)])*(1-A)
    
    j <- c(1:k)
    b1 <- sum(sapply(j, function(j)j*(j-1)*Q(j, x)))
    b2 <- sum(sapply(j, function(j)j*Q(j, x)))
    gamma_infreq_square <- max(D_infreq/C_infreq*t/(t - 1)*b1/b2/(b2) - 1, 0)
    CV_infreq <- sqrt(gamma_infreq_square)
    D_freq <- length(x[which(x > k)])
    
    BASIC.DATA <- matrix(paste(c("D", "t", "k", "D_infreq", "C_infreq", "CV_infreq", "D_freq"),
                               c(D,t,k,D_infreq,C_infreq,CV_infreq,D_freq),
                               sep = "="), ncol=1)
    colnames(BASIC.DATA)=c("Value")
    rownames(BASIC.DATA)=c("Number of observed species","Number of sample/quadrats","Cut-off point",
                           "Number of observed species for infrequent species","Estimated sample coverage for infrequent species",
                           "Estimated CV for infrequent species",
                           "Number of observed species for frequent species")
    return(list(BASIC.DATA, D, t, D_infreq, C_infreq, CV_infreq, D_freq))
  }
  D <- basicInci(data, k)[[2]]
  D_infreq <- basicInci(data, k)[[4]]
  C_infreq <- basicInci(data, k)[[5]]
  CV_infreq <- basicInci(data, k)[[6]]
  D_freq <- basicInci(data, k)[[7]]
  
  u <- c(1:k)   
  n_infreq <- sum(x[which(x <= k)])
  si <- sum(sapply(u, function(u)u*(u-1)*Q(u, x)))
  data.f <- data[which(x <= k), ]
  nd <- as.numeric(apply(data.f, 2, sum))
  nd_c <- nd[which(nd != 0)]
  e <- c(1:length(nd_c))
  o <- rep(e ,each = length(e))
  p <- rep(e ,length(e))    
  s <- sum(mapply(function(o, p)nd_c[o]*nd_c[p], o, p)) - sum(sapply(e, function(e)nd_c[e]*nd_c[e]))
  S_Model_TH <- function(x, k){
    si <- sum(sapply(u, function(u)u*(u - 1)*Q(u, x)))
    gamma_infreq_square_th <- max(D_infreq/C_infreq*si/s - 1, 0)
    s_Model_th <- D_freq + D_infreq/C_infreq + Q(1, x)/C_infreq*gamma_infreq_square_th
    CV_infreq_th <- sqrt(gamma_infreq_square_th)  
    return(unlist(list(s_Model_th, CV_infreq_th)))
  }
  s_Model_th <- S_Model_TH(x, k)[1]
  CV_infreq_th <- S_Model_TH(x, k)[2]
  #### differential ####
  diff <- function(q){
    if (CV_infreq_th != 0){
      if ( q == 1) {
        dc_infreq <-  - (n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x))*2*Q(1, x)*(t - 1) - 
                           (t - 1)*Q(1, x)^2*((t - 1)*(Q(1, x) + n_infreq) + 2*Q(2, x)))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 + #g2
          (C_infreq^2*(D_infreq*si + Q(1, x)*si) - #g3
             Q(1, x)*D_infreq*si*(2*C_infreq*dc_infreq)             
          )/C_infreq^4/s - 
          (C_infreq - Q(1, x)*dc_infreq)/C_infreq^2 #g4
      } else if (q == 2) {
        dc_infreq <-  - ( - (t - 1)*Q(1, x)^2*(2*(t - 1)*Q(1, x) + 2*(n_infreq + 2*Q(2, x))))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 + #g2
          (C_infreq^2*Q(1, x)*(si + 2*D_infreq) - Q(1, x)*D_infreq*si*( #g3
            2*C_infreq*dc_infreq)
          )/C_infreq^4/s - 
          ( - Q(1, x)*dc_infreq)/C_infreq^2 #g4
      } else if(q > k) {
        d <- 1
      } else {
        dc_infreq <-  - ( - (t - 1)*Q(1, x)^2*((t - 1)*Q(1, x)*q + 2*Q(2, x)*q))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 + #g2
          (C_infreq^2*Q(1, x)*(si + q*(q - 1)*D_infreq) - Q(1, x)*D_infreq*si*( #g3
            2*C_infreq*dc_infreq)
          )/C_infreq^4/s - 
          ( - Q(1, x)*dc_infreq)/C_infreq^2 #g4
      }
      return(d)
    } else {
      if ( q == 1) {
        dc_infreq <-  - (n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x))*2*Q(1, x)*(t - 1) - 
                           (t - 1)*Q(1, x)^2*((t - 1)*(Q(1, x) + n_infreq) + 2*Q(2, x)))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 #g2
      } else if (q == 2) {
        dc_infreq <-  - ( - (t - 1)*Q(1, x)^2*(2*(t - 1)*Q(1, x) + 2*(n_infreq + 2*Q(2, x))))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 #g2
      } else if(q > k) {
        d <- 1
      } else {
        w <- c(q:k)
        ss <- sum(sapply(w, function(w)nd[w]))
        dc_infreq <-  - ( - (t - 1)*Q(1, x)^2*((t - 1)*Q(1, x)*q + 2*Q(2, x)*q))/(n_infreq*((t - 1)*Q(1, x) + 2*Q(2, x)))^2
        d <- (C_infreq - D_infreq*dc_infreq)/C_infreq^2 #g2
      }
      return(d)
    }
  }
  
  COV.q <- function(i,j){
    if (i == j){
      cov.q <- Q(i, dat)*(1 - Q(i, dat)/s_Model_th)
    } else {
      cov.q <- -Q(i, dat)*Q(j, dat)/s_Model_th
    }     
    return(cov.q)
  }
  
  i <- rep(sort(unique(x)),each = length(unique(x)))
  j <- rep(sort(unique(x)),length(unique(x)))       # all combination
  
  var_th <- sum(mapply(function(i, j)diff(i)*diff(j)*COV.q(i, j), i, j))
  ######################
  if (round(s_Model_th - D, 5) != 0){
    C <- exp(z*sqrt(log(1+var_th/(s_Model_th - D)^2)))
    CI_Model_th <- c(D + (s_Model_th - D)/C, D + (s_Model_th - D)*C)
  } else {
    i <- c(1:max(x))
    i <- i[unique(x)]
    var_obs <- sum(sapply(i, function(i)Q(i, x)*(exp(-i) - exp(-2*i)))) - 
      (sum(sapply(i, function(i)i*exp(-i)*Q(i, x))))^2/t
    P <- sum(sapply(i, function(i)Q(i, x)*exp(-i)/D))
    CI_Model_th <- c(max(D, D/(1 - P) - z*sqrt(var_obs)/(1 - P)), D/(1 - P) + z*sqrt(var_obs)/(1 - P))  
  }
  table <- matrix(c(s_Model_th, sqrt(var_th), CI_Model_th), ncol = 4)
  colnames(table) <- c("Estimate", "Est_s.e.", paste(conf*100,"% Lower Bound"), paste(conf*100,"% Upper Bound"))
  rownames(table) <- "Model(th) (Lee & Chao, 1994)"
  return(list(table, CV_infreq_th))
}