conservation.R

# Misc functions for conservation biology stats in R.

shannon <- function (x) {
  proportion_x = x/sum(x)
  print(proportion_x)
  print(log(proportion_x))
  print(proportion_x * log(proportion_x))
  print(sum(proportion_x * log(proportion_x)))
  return(-sum(proportion_x*log(proportion_x)))
}

hills <- function (x) {
  return(exp(shannon(x)))
}

simpson <- function (x) {
  p = x/sum(x)
  ans = 1/sum(p^2)
  return(ans)
}

a <- c(120, 120, 120, 120)
b <- c(78, 80, 76, 78, 78, 78, 77)
c <- c(623, 17, 12, 24, 7, 18, 6)
d <- c(470, 34, 22, 25)
e <- c(17, 31, 7, 12, 42, 29)

whitaker <- function(x, total) {
  alpha = mean(x)
  print(alpha)
  beta = total/alpha - 1
  return(beta)
}

whit_a <- c( 7, 8, 8, 6, 7, 7)
whit_b <- c(22, 12, 4, 7, 15, 8)
whit_c <- c(46, 50, 51, 39, 44, 43)

tot_a <- 9
tot_b <- 34
tot_c <- 71

whitaker(whit_a, tot_a)
whitaker(whit_b, tot_b)
whitaker(whit_c, tot_c)