R/hillN2.R

In dempseydanielle/marindicators: Marine Ecosystem and Fishing Pressure Indicators

#'@title Calculates Hill's Species Dominance (N2)
#'@description This function calculates Hill's Species Dominance (N2) for
#'  \eqn{j} areas and \eqn{i} years.
#'@details  Hill's Species Dominance (HillN2): \deqn{HillN2 = 1/\Sigma p_i^2}
#'  \eqn{p_i} is the proportion of the total sample contributed by the i(th)
#'  species. HillN2 is the inverse of the Simpson's index. This index is
#'  sensitive to the evenness of the distribution of individuals between species
#'  (Hill, 1973).
#'@inheritParams shannon
#'@return Returns a dataframe with columns \code{ID} and \code{YEAR}, and a
#'  column \code{HillDominance_group} for each entry in \code{groups}.
#'
#'  If there is no data for spatial scale \eqn{j} in year \eqn{i}, indicator
#'  values is assigned NA.
#'@family biodiversity indicators
#'@references  Bundy A, Gomez C, Cook AM. 2017. Guidance framework for the
#'  selection and evaluation of ecological indicators. Can. Tech. Rep. Fish.
#'  Aquat. Sci. 3232: xii + 212 p.
#'
#'  Greenstreet SP, Rogers SI. 2006. Indicators of the health of the North Sea
#'  fish community: identifying reference levels for an ecosystem approach to
#'  management. ICES J Mar Sci J du Cons 63:573-593
#'
#'  Hill MO. 1973. Diversity and evenness: a unifying notation and its
#'  consequences. Ecology 54: 427-431.
#'@author  Danielle Dempsey, Adam Cook \email{Adam.Cook@@dfo-mpo.gc.ca},
#'  Catalina Gomez, Alida Bundy
#'@examples
#'data(X)
#'hillN2(X, groups = "ALL", metric = "ABUNDANCE", years = c(2014:2019))
#'@export


hillN2 <- function(X, groups, species.table = NULL, metric = "ABUNDANCE", years)  {
  
  for(k in 1:length(groups)){          # loop over species groups
    
    X.k <- speciesGroups(X = X, group = groups[k], species.table = species.table) # subset X to the species of interest
    uI = unique(X$ID)                   # extract the spatial scale ID's
    ind.k <- NULL                       # initialize dataframe for storing indicator values
    
    for (j in 1:length(uI)){            # loop over all spatal scales
      
      X.j = X.k[X.k$ID == uI[j], ]          # subset data to spatial scale j
      
      for (i in 1:length(years)){                     # loop over each year
        
        year.i = years[i]                             # set years.i to current year  
        X.ij = X.j[X.j$YEAR == year.i, metric]        # subset data to include only current year
        
        if(length(X.ij) > 0){
          X.ij = X.ij[order(X.ij)]                         # order from smallest to largest (not required)
          p <- X.ij/sum(X.ij)                              # calculate proportion of each species by metric
          ind.i <- 1/sum(p^2)                              # calculate Hill's species dominance
        } else ind.i <- NA
        
        ind.i = data.frame(uI[j], year.i, ind.i)     # create a dataframe with spatial scale ID, year, and indicator value
        ind.k = rbind(ind.k, ind.i)                  # bind ind.i to ind dataframe
      }
    }
    
    ind.name <- paste("HillDominance_", groups[k], sep = "")            # name indicator: HillDominance_group
    names(ind.k) = c("ID", "YEAR", ind.name)                            # name the ind dataframe
    ind.k <- ind.k[order(ind.k$ID), ] 
    
    if(k == 1) ind = ind.k
    
    ind <- merge(ind, ind.k)
  }
  
  ind                                              # return Hill's species dominance
}