R: Minimal Spanning Tree

mstree {ade4} | R Documentation

## Minimal Spanning Tree

### Description

Minimal Spanning Tree

### Usage

    mstree(xdist, ngmax = 1)

### Arguments

`xdist` | an object of class `dist` containing an observed dissimilarity
`ngmax` | a component number (default=1). Select 1 for getting classical MST. To add n supplementary edges k times: select k+1.

### Value

returns an object of class `neig`

### Author(s)

Daniel Chessel

### Examples

    data(mafragh)
    maf.coa <- dudi.coa(mafragh$flo, scan = FALSE)
    maf.mst <- ade4::mstree(dist.dudi(maf.coa), 1)

    if(adegraphicsLoaded()) {
      g0 <- s.label(maf.coa$li, plab.cex = 0, ppoints.cex = 2, nb = neig2nb(maf.mst))
    } else {
      s.label(maf.coa$li, clab = 0, cpoi = 2, neig = maf.mst, cnei = 1)
    }

    xy <- data.frame(x = runif(20), y = runif(20))

    if(adegraphicsLoaded()) {
      g1 <- s.label(xy, xlim = c(0, 1), ylim = c(0, 1),
        nb = neig2nb(ade4::mstree(dist.quant(xy, 1), 1)), plot = FALSE)
      g2 <- s.label(xy, xlim = c(0, 1), ylim = c(0, 1),
        nb = neig2nb(ade4::mstree(dist.quant(xy, 1), 2)), plot = FALSE)
      g3 <- s.label(xy, xlim = c(0, 1), ylim = c(0, 1),
        nb = neig2nb(ade4::mstree(dist.quant(xy, 1), 3)), plot = FALSE)
      g4 <- s.label(xy, xlim = c(0, 1), ylim = c(0, 1),
        nb = neig2nb(ade4::mstree(dist.quant(xy, 1), 4)), plot = FALSE)
      G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))

    } else {
      par(mfrow = c(2, 2))
      for(k in 1:4) {
        neig <- mstree(dist.quant(xy, 1), k)
        s.label(xy, xlim = c(0, 1), ylim = c(0, 1), addax = FALSE, neig = neig)
      }
    }

[Package ade4 version 1.7-15 Index]