Minimum Spanning Tree

Josh, I would recommend to use a package that supports networks, e.g.
igraph, but there are others as well.

You can read in the data using 'read.csv()', transform it to a matrix
with 'as.matrix()', and then create an igraph object from it with
'graph.adjacency()'.

Then call 'minimum.spanning.tree()' to calculate the tree and 'plot()'
to plot it. E.g. for your example file:

library(igraph)
D <- read.csv("/tmp/matrix.csv")
D <- D[,-1]       # we don't need the first column
G <- graph.adjacency(as.matrix(D), weighted=TRUE)

## Some graphical parameters
V(G)$label <- V(G)$name
V(G)$shape <- "rectangle"
V(G)$color <- "white"
V(G)$size <- 40

## MST and plot
mst <- minimum.spanning.tree(G)
lay <- layout.reingold.tilford(G, mode="all")
plot(mst, layout=lay)

Best,
Gabor

Minimum Spanning Tree

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