R/bgdispersal.R

In vegan: Community Ecology Package

bgdispersal <- function (mat, PAonly = FALSE, abc = FALSE) 
{
    mat <- as.matrix(mat)
    names <- rownames(mat)
    if (sum((mat - decostand(mat, "pa"))) == 0) {
        PAonly <- TRUE
        mat1 <- mat
    }
    else {
        mat1 <- decostand(mat, "pa")
        if (PAonly == FALSE) mat2 <- mat
    }
    n <- nrow(mat)
    p <- ncol(mat)
    a <- mat1 %*% t(mat1)
    b <- mat1 %*% (1 - t(mat1))
    c <- (1 - mat1) %*% t(mat1)
    d <- ncol(mat1) - a - b - c
    DD1 <- (a * (b - c))/((a + b + c)^2)
    DD2 <- (2 * a * (b - c))/((2 * a + b + c) * (a + b + c))
    ## McNemar <- (abs(b - c) - 1)^2/(b + c)     # Old code
    ## diag(McNemar) <- 0                        # Old code
    McNemar <- matrix(NA, n, n, dimnames=list(names,names))
    pP.Mc <- matrix(NA, n, n, dimnames=list(names,names))
    for (j in 1:(n - 1)) {
        for (jj in (j + 1):n) {
            bb = b[j, jj]
            cc = c[j, jj]
            if ((bb + cc) == 0) {
                McNemar[j, jj] = 0
                pP.Mc[j, jj] = 1
            } else {
                if(bb == 0) { B = 0 } else { B = bb*log(bb) }
                if(cc == 0) { C = 0 } else { C = cc*log(cc) }
                ## Williams correction
                q = 1 + 1/(2*(bb+cc))
                ## McNemar = 2*(b*log(b) + c*log(c) - (b+c)*log((b+c)/2))
                McNemar[j, jj] = 2*(B + C - (bb+cc)*log((bb+cc)/2)) / q
                pP.Mc[j, jj] <- pchisq(McNemar[j, jj], 1, lower.tail = FALSE)
                if ((b[j, jj] + c[j, jj]) == 0) 
                    pP.Mc[j, jj] <- 1
            }
        }
    }
    if (!PAonly) {
        DD3 <- matrix(0, n, n, dimnames=list(names,names))
        DD4 <- matrix(0, n, n, dimnames=list(names,names))
        row.sum <- apply(mat2, 1, sum)
        for (j in 1:(n - 1)) {
            for (jj in (j + 1):n) {
                W <- sum(apply(mat2[c(j, jj), ], 2, min))
                A <- row.sum[j]
                B <- row.sum[jj]
                temp3 <- W * (A - B)/((A + B - W)^2)
                temp4 <- 2 * W * (A - B)/((A + B) * (A + B - W))
                DD3[j, jj] <- temp3
                DD3[jj, j] <- -temp3
                DD4[j, jj] <- temp4
                DD4[jj, j] <- -temp4
            }
        }
        out <- list(DD1 = DD1, DD2 = DD2, DD3 = DD3, DD4 = DD4, 
                    McNemar = McNemar, prob.McNemar = pP.Mc)
    }
    else {
        out <- list(DD1 = DD1, DD2 = DD2, McNemar = McNemar, 
                    prob.McNemar = pP.Mc)
    }
    if (abc) {
        out$a <- a
        out$b <- b
        out$c <- c
    }
    out
}