Analysis of community ecology data in R

Evaluates, if the sample has appropriate group membership. Samples with high s value are well clustered, s value around zero means that the sample is between two clusters, and negative s value means that the sample has been misclassified.

For example, we will use results of beta flexible numerical classification of vltava.spe data (see agnes (library cluster)):

## Example of silhouette function
 
## Following code is not necessary, if you already used examples above...
# library (cluster)
# dis <- vegdist (sqrt (vltava.spe), method = 'bray') # percentage cover data are transformed by square root
# cluster.flexible <- agnes (x = dis, method = 'flexible', par.method = 0.625)
# cluster.flexible.hclust <- as.hclust (cluster.flexible)
 
cl <- cutree (cluster.flexible.hclust, k = 5)
si <- silhouette (cl, dis)
plot (si)
 
# Group 3 has the highest number of missclassified samples, on the other hand groups 1, 2 and 5 are well defined. 

# Comparison of silhouettes for single linkage, complete average linkage method.
# dis <- vegdist (sqrt (vltava.spe), method = 'bray') # percentage cover data are transformed by square root
# cluster.single <- hclust (d = dis, method = 'single')
# cluster.complete <- hclust (dis, 'complete')
# cluster.average <- hclust (dis, 'average')
 
par (mfrow = c(1,3))
plot (silhouette (cutree (cluster.single, k = 5), dis))
plot (silhouette (cutree (cluster.complete, k = 5), dis))
plot (silhouette (cutree (cluster.average, k = 5), dis))