clValid (version 0.7)

dunn: Dunn Index

Description

Calculates the Dunn Index for a given clustering partition.

Usage

dunn(distance = NULL, clusters, Data = NULL, method = "euclidean")

Arguments

distance

The distance matrix (as a matrix object) of the clustered observations. Required if Data is NULL.

clusters

An integer vector indicating the cluster partitioning

Data

The data matrix of the clustered observations. Required if distance is NULL.

method

The metric used to determine the distance matrix. Not used if distance is provided.

Value

Returns the Dunn Index as a numeric value.

Details

The Dunn Index is the ratio of the smallest distance between observations not in the same cluster to the largest intra-cluster distance. The Dunn Index has a value between zero and infinity, and should be maximized. For details see the package vignette.

References

Dunn, J.C. (1974). Well separated clusters and fuzzy partitions. Journal on Cybernetics, 4:95-104.

Handl, J., Knowles, K., and Kell, D. (2005). Computational cluster validation in post-genomic data analysis. Bioinformatics 21(15): 3201-3212.

See Also

For a description of the function 'clValid' see clValid.

For a description of the class 'clValid' and all available methods see clValidObj or clValid-class.

For additional help on the other validation measures see dunn, stability, BHI, and BSI.

Examples

# NOT RUN {
data(mouse)
express <- mouse[1:25,c("M1","M2","M3","NC1","NC2","NC3")]
rownames(express) <- mouse$ID[1:25]
## hierarchical clustering
Dist <- dist(express,method="euclidean")
clusterObj <- hclust(Dist, method="average")
nc <- 2 ## number of clusters      
cluster <- cutree(clusterObj,nc)
dunn(Dist, cluster)
# }