R: K-Medoids Partitions of Clusterings

cl_pam {clue} | R Documentation

## K-Medoids Partitions of Clusterings

### Description

Compute k-medoids partitions of clusterings.

### Usage

    cl_pam(x, k, method = "euclidean", solver = c("pam", "kmedoids"))

### Arguments

`x` | an ensemble of partitions or hierarchies, or something coercible to that (see `cl_ensemble`).
`k` | an integer giving the number of classes to be used in the partition.
`method` | a character string or a function, as for argument `method` of function `cl_dissimilarity`.
`solver` | a character string indicating the k-medoids solver to be employed. May be abbreviated. If `"pam"` (default), the Partitioning Around Medoids (Kaufman & Rousseeuw (1990), Chapter 2) heuristic `pam` of package cluster is used. Otherwise, the exact algorithm of `kmedoids` is employed.

### Details

An optimal k-medoids partition of the given cluster ensemble is defined as a partition of the objects x_i (the elements of the ensemble) into k classes C_1, …, C_k such that the criterion function L = ∑_{l=1}^k \min_{j \in C_l} ∑_{i \in C_l} d(x_i, x_j) is minimized.

Such secondary partitions (e.g., Gordon & Vichi, 1998) are obtained by computing the dissimilarities d of the objects in the ensemble for the given dissimilarity method, and applying a dissimilarity-based k-medoids solver to d.

### Value

An object of class `"cl_pam"` representing the obtained “secondary” partition, which is a list with the following components.

`cluster` | the class ids of the partition.
`medoid_ids` | the indices of the medoids.
`prototypes` | a cluster ensemble with the k prototypes (medoids).
`criterion` | the value of the criterion function of the partition.
`description` | a character string indicating the dissimilarity method employed.

### References

L. Kaufman and P. J. Rousseeuw (1990). Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York.

A. D. Gordon and M. Vichi (1998). Partitions of partitions. Journal of Classification, 15, 265–285. doi: 10.1007/s003579900034.

### See Also

`cl_pclust` for more general prototype-based partitions of clusterings.

### Examples

    data("Kinship82")
    party <- cl_pam(Kinship82, 3, "symdiff")
    ## Compare results with tables 5 and 6 in Gordon & Vichi (1998).
    party
    lapply(cl_prototypes(party), cl_classes)
    table(cl_class_ids(party))

[Package clue version 0.3-54 Index]