R/diversity.R

In vegan: Community Ecology Package

`diversity` <-
  function (x, index = "shannon", MARGIN = 1, base = exp(1)) 
{
    x <- drop(as.matrix(x))
    INDICES <- c("shannon", "simpson", "invsimpson")
    index <- match.arg(index, INDICES)
    if (length(dim(x)) > 1) {
        total <- apply(x, MARGIN, sum)
        x <- sweep(x, MARGIN, total, "/")
    } else {
        x <- x/sum(x)
    }
    if (index == "shannon")
        x <- -x * log(x, base)
    else
        x <- x*x
    if (length(dim(x)) > 1) 
        H <- apply(x, MARGIN, sum, na.rm = TRUE)
    else
        H <- sum(x, na.rm = TRUE)
    if (index == "simpson") 
        H <- 1 - H
    else if (index == "invsimpson") 
        H <- 1/H
    H
}