spantree finds a minimum spanning tree
connecting all points, but disregarding dissimilarities that are at or
above the threshold or NA.spantree(d, toolong = 0)
## S3 method for class 'spantree':
cophenetic(x)
spandepth(x)
## S3 method for class 'spantree':
plot(x, ord, cex = 0.7, type = "p", labels, dlim,
FUN = sammon, ...)
## S3 method for class 'spantree':
lines(x, ord, display="sites", ...)dist or
a an object, such as a matrix, that can be converted to a
dissimilarity matrix. Functions vegdist and
NA.
The function uses a fuzz factor, so
that dissimilarities close to the limit will be made NA, too.
If toolong = 0 (or negative), no dissimilarity is regarded
as tspantree result object.scores.type="p" or type="b", or as text label with
type="t". The tree (lines) will always be plotted.type="t" or node names if this is
missing.cophenetic dissimilarity.scores used for ord.spantree
returns an object of class spantree which is a
list with two vectors, each of length $n-1$. The
number of links in a tree is one less the number of observations, and
the first item is omitted. The items areNA
and tree is disconnected at the node.kid = NA, then
dist = 0.spantree finds a minimum spanning tree for
dissimilarities (there may be several minimum spanning trees, but the
function finds only one). Dissimilarities at or above the threshold
toolong and NAs are disregarded, and the spanning tree
is found through other dissimilarities. If the data are disconnected,
the function will return a disconnected tree (or a forest), and the
corresponding link is NA. Connected subtrees can be identified
using distconnected. Function cophenetic finds distances between all points along
the tree segments. Function spandepth returns the depth of
each node. The nodes of a tree are either leaves (with one link) or
internal nodes (more than one link). The leaves are recursively
removed from the tree, and the depth is the layer at with the leaf
was removed. In disconnected spantree object (in a forest)
each tree is analysed separately and disconnected nodes not in any
tree have depth zero.
Function plot displays the tree over a
supplied ordination configuration, and lines adds a spanning
tree to an ordination graph. If configuration is not supplied for plot,
the function ordinates the cophenetic dissimilarities of the
spanning tree and overlays the tree on this result. The default
ordination function is sammon (package dlim, and sometimes the results will remain
twisted). These ordination methods do not work with disconnected
trees, but you must supply the ordination configuration. Function
lines will overlay the tree in an existing plot.
Function spantree uses Prim's method
implemented as priority-first search for dense graphs (Sedgewick
1990). Function cophenetic uses function
stepacross with option path = "extended". The
spantree is very fast, but cophenetic is slow in very
large data sets.
vegdist or dist for getting
dissimilarities, and hclust or
agnes for single linkage clustering.data(dune)
dis <- vegdist(dune)
tr <- spantree(dis)
## Add tree to a metric scaling
plot(tr, cmdscale(dis), type = "t")
## Find a configuration to display the tree neatly
plot(tr, type = "t")
## Depths of nodes
depths <- spandepth(tr)
plot(tr, type = "t", label = depths)Run the code above in your browser using DataLab