R/shannon.R

Defines functions shannon

Documented in shannon

#' Get alpha diversity using shannon
#'
#' @param x A list of counts
#' @return A single value
#'
#' @examples
#' shannon(seq_len(10))
#'
#' @export

# x: Species count vector
shannon <- function(x) {
    # Ignore zeroes
    x <- x[x > 0]
    
    # Species richness (number of species)
    S <- length(x)
    
    # Relative abundances
    p <- x / sum(x)
    
    # Shannon index
    (-sum(p * log(p)))
}
compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.