R/postMDS.R

In vegandevs/vegan: Community Ecology Package

`postMDS` <-
    function (X, dist, pc = TRUE, center = TRUE, halfchange,
              threshold = 0.8, nthreshold = 10, plot = FALSE, ...)
{
    Size <- attr(dist, "Size")
    if (any(names(X) == "points"))
        x <- X$points
    else x <- as.matrix(X)
    if (center)
        x <- scale(x, scale = FALSE)
    if (pc) {
        dn <- dimnames(x)
        x <- prcomp(x, center = center)$x
        dimnames(x) <- dn
    }
    ## Check halfchange scaling, if not explicitly defined
    maxdist <- attr(dist, "maxdist")
    if (missing(halfchange)) {
        ## play safe: if 'maxdist' is missing or NA, skip halfchange
        ## scaling. vegdist sets attr maxdist, and for other distfuns,
        ## metaMDSdist tries to find maxdist. Dissimilarity input may
        ## not have this attribute and are not halfchange scaled.
        if (!is.null(maxdist) && !is.na(maxdist) && is.numeric(maxdist))
            halfchange <- TRUE
        else
            halfchange <- FALSE
    }
    if (halfchange) {
        dist <- as.vector(dist)
        ordi <- as.vector(vegdist(x, "euclidean"))
        ## adjust threshold to maxdist if available
        if (!is.numeric(maxdist))
            warning("halfchange requested, but ceiling distance is unknown, using ", threshold)
        else {
            threshold <- maxdist * threshold
            ## something fishy - similarities instead of distances?
            if (threshold < sqrt(.Machine$double.eps))
                warning("dubious maxdist ", maxdist, ": similarities instead of dissimilarities?")
        }
        take <- dist < threshold
        if (sum(take) < nthreshold) {
            warning("skipping half-change scaling: too few points below threshold")
            halfchange <- FALSE
        }
        else {
            k <- coef(lm(dist[take] ~ ordi[take]))
            names(k) <- NULL
            hc <- (1 - k[1])/2/k[2]
            x <- x/hc
        }
    }
    if (!halfchange) {
        hc <- max(dist(x, "euclidean"))/max(dist, na.rm = TRUE)
        x <- x/hc
    }
    if (plot && halfchange) {
        cross.lim <- 45
        if (Size > cross.lim)
            pch <- "."
        else pch <- "+"
        orange <- range(c(ordi, 0, 1))
        drange <- range(c(dist, 0, 1))
        plot(orange, drange, type = "n", xlab = "Ordination distance",
             ylab = "Community dissimilarity")
        ## Colours in default palette: 2 = red, 4 = blue, 8 = gray.
        points(ordi[take], dist[take], pch = pch, col = 4)
        points(ordi[!take], dist[!take], pch = pch, col = 8)
        abline(h = threshold)
        abline(h = k[1])
        hclevel <- (1 - k[1])/2 + k[1]
        segments(0, hclevel, hc, hclevel, col = 2, lwd = 2)
        arrows(hc, hclevel, hc, 0, col = 2, lwd = 2)
        arrows(0, k[1], 0, hclevel, col = 2, code = 3)
        arrows(0, hclevel, 0, 1, col = 2, code = 3)
        j <- 0.02
        text(0 + j, threshold + j, "Threshold", adj = c(0, 0))
        text(0 + j, k[1] + j, "Replicate dissimilarity", adj = c(0,
                                                         0))
        text(0 + j, hclevel + j, "Half-change", adj = c(0, 0))
        abline(k, col = 4, lwd = 2)
    }
    attr(x, "centre") <- center
    attr(x, "pc") <- pc
    attr(x, "halfchange") <- halfchange
    attr(x, "internalscaling") <- hc
    if (any(names(X) == "points"))
        X$points <- x
    else X <- x
    X
}