R/bcdist.R

In phiala/ecodist: Dissimilarity-Based Functions for Ecological Analysis

bcdist <- function(x, rmzero = FALSE)
{

# Calculates Bray-Curtis distance (1 - percent similarity) for the
# rows of a matrix.
# 
# If rmzero = TRUE, all empty rows of the matrix will be removed before calculating
# distances. Otherwise the distance between empty rows will be set to 0.
#
# Sarah C. Goslee, November 1997
#
# The same functionality appears in distance(), but bcdist is substantially faster.

    x <- as.matrix(x)
    if(rmzero == TRUE) {
        xsum <- apply(x, 1, sum)
        x <- x[xsum > 0,  ]
    }
    dist.v <- rep(0, (nrow(x) * (nrow(x) - 1))/2)    

   cresults <- .C("bcdistc",
        as.double(as.vector(t(x))),
        as.integer(nrow(x)),
        as.integer(ncol(x)),
        dist.v = as.double(dist.v),
        PACKAGE = "ecodist")
    dist.v <- cresults$dist.v

    ## give the results attributes similar to dist()
    attr(dist.v, "Size") <- nrow(x)
      attr(dist.v, "Labels") <- rownames(x)
     attr(dist.v, "Diag") <- FALSE
     attr(dist.v, "Upper") <- FALSE
    attr(dist.v, "method") <- "bray-curtis"
    class(dist.v) <- "dist"

    dist.v
}