R/sp.assoc.R

In helixcn/spaa: SPecies Association Analysis

sp.assoc <-
  function(matr) {
    if (any(is.na(matr))) {
      matr <- na.omit(matr)
      cat("The data matrix contains NA, and have been removed.\n")
    }
    matr[matr > 1] <- 1
    frq <- freq.calc(matr)
    N <- nrow(matr) ## Number of plots
    S <- ncol(matr) ## Number of species
    n <-
      apply(matr, 2, sum) ## Number of plots occupied by certain species
    Tj <-
      apply(matr, 1, sum) ## Total number of species for each plot
    t <- mean(Tj) ## Mean species number for all the plots
    STsq <- (1 / N) * sum((Tj - t)^2) ## Variance of species number
    sigmaTsq <-
      sum((1 - frq) * frq) ## Variance of species relative frequency
    VR <-
      STsq / sigmaTsq ## Variance ratio: VR>1 Positively associated, VR<1 Negative associated
    W <- VR * N # W statistic value, used in comparison with Chi(n).
    result <- list(
      pi = frq,
      N = N,
      S = S,
      Tj = Tj,
      Numspmean = t,
      sigmaTsq = sigmaTsq,
      STsq = STsq,
      var.ratio = VR,
      W = W
    )
    return(result)
  }