R/cal_taxo.div.R

In kun-ecology/ecoloop: Loop for ecological data analysis

#' Calculte taxonomic diversity
#'
#' @param spe.df a dataframe, row as site while column as species name, nonumeric data will be used in final results
#'
#' @return a dataframe, Species number, Shannon-wiener diversity, Simpson diversity and Evenness are calculated
#' @export
#'
#' @examples
cal_taxo.div <- function(spe.df){
  # species number
  spe <- spe.df[,sapply(spe.df,is.numeric)]
  S <- vegan::specnumber(spe)
  # H: Shannon-wiener diveristy,base=exp(1)
  H <- vegan::diversity(spe,index = "shannon")
  # D: Simpson diveristy
  D <- vegan::diversity(spe,index = "simpson")
  # E: eveness,Evenness is a measure of how homogeneous or even a community or ecosystem is in terms of the abundances of its species.
  # A community in which all species are equally common is considered even and has a high degree of evenness.
  E <- D/log(S)
  div <- data.frame(Shannon_div=H,Simpson_div=D,
                    Evenness=E, Species_num=S) %>%
    cbind(spe.df[,!(sapply(spe.df,is.numeric))],.)
  return(div)

}