R/isomap.R

In vegandevs/vegan: Community Ecology Package

`isomap` <-
function(dist, ndim=10, ...)
{
    dist <- isomapdist(dist, ...)
    out <- wcmdscale(dist, k=ndim, eig=TRUE)
    ## some versions of cmdscale may return NaN points corresponding
    ## to negative eigenvalues.
    if ((naxes <- sum(out$eig > 0)) < ndim && naxes) {
        out$points <- out$points[, seq(naxes), drop = FALSE]
        message(gettextf("isomap returns only %d axes with positive eigenvalues",
                         naxes))
    }
    npoints <- nrow(out$points)
    net <- matrix(FALSE, nrow=npoints, ncol=npoints)
    net[lower.tri(net)][attr(dist, "net")] <- TRUE
    net <- which(net, arr.ind=TRUE)
    out$method <- attr(dist, "method")
    out$criterion <- attr(dist, "criterion")
    out$critval <- attr(dist, "critval")
    out$take <- attr(dist, "take")
    out$net <- net
    out$npoints <- npoints
    out$call <- match.call()
    class(out) <- "isomap"
    out
}