R/cscore.R

In ECGen/ComGenR: Functions for COMmunity GENetics analyses in R

#' Calculates the C-Score of Stone and Roberts 1991.
#' 
#' Calculates the C-Score of Stone and Roberts 1991.
#' 
#' 
#' @param x Community matrix of species abundances or present absences with
#' species in columns.
#' @param cu.mat Logical: should the checkerboard unit matrix be returned?
#' @return %% ~Describe the value returned %% If it is a LIST, use %%
#' @export cscore
#' @note %% ~~further notes~~
#' @author Matthew K. Lau
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#' 
#' ##---- Should be DIRECTLY executable !! ----
#' ##-- ==>  Define data, use random,
#' ##--	or do  help(data=index)  for the standard data sets.
#' 
cscore <- function(x, cu.mat = FALSE){
    x[x != 0] <- 1 #force binary
    cu <- matrix(0,nrow=ncol(x),ncol=ncol(x))
    for (i in 1:ncol(x)){
        for (j in 1:ncol(x)){
            ri <- sum(x[,i])
            rj <- sum(x[,j])
            S <- x[,i]*0
            S[x[,i]==1&x[,j]==1] <- 1
            S <- sum(S)
            cu[i,j] <- (ri-S)*(rj-S)
        }
    }
    if (cu.mat){return(cu)}else{return(mean(cu))}
}