Produce a Silhouette Object From a Partana, Clustering, or Stride Object
Extracts components from a partana, clustering, or stride object,
and passes the values to the silhouette function to
produce an object of class silhouette.
## S3 method for class 'partana' silhouette(x, dist, ...) ## S3 method for class 'clustering' silhouette(x, dist, ...) ## S3 method for class 'stride' silhouette(x, dist, ...) testsil(sil)
x |
an object of class ‘partana’, ‘clustering’, or ‘stride’ |
dist |
an object of class dist |
... |
miscellaneous arguments to pass to function silhouette |
sil |
an object of class ‘silhouette’ |
For ‘partana’ and ‘clustering’ objects the advantage over
calling silhouette directly is that the row.names of the resulting
object are added to the results, as opposed to consecutive integers.
For objects of class ‘stride’ the function extracts the component
‘clustering’ for each level of a stride object, and calls function
silhouette in library ‘cluster’
returniung the mean silhouette width for each case.
testsil identifies ‘misfits’ in a partition, defined as plots with
a negative silhouette width, and prints them out in a sorted list.
An object of class silhouette
This is a a simple conversion routine to allow plotting a silhouette plot for an object of class partana.
David W. Roberts droberts@montana.edu
data(shoshveg) # produces a data frame of vegetation data,
#samples as rows, attributes as columns
dis.bc <- dsvdis(shoshveg,'bray/curtis') # produces a Bray/Curtis
# dissimilarity matrix
opt.5 <- optpart(5,dis.bc) # produces an optimal partitioning into
# 5 clusters
silhouette(opt.5,dis.bc) # calculates the silhouette values
## Not run: plot(silhouette(opt.5,dis.bc)) # produce silhouette
# plot on current devicePlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.