compClust {clues} | R Documentation |
Compare different partitions for a data set based on agreement indices, average sihouette index and CH index.
compClust(y, memMat, disMethod = "Euclidean")
y |
data matrix which is an R matrix object (for dimension > 1) or vector object (for dimension = 1) with rows being observations and columns being variables. |
memMat |
cluster membership matrix. Each column corresponds to a partition
of the matrix |
disMethod |
specification of the dissimilarity measure. The available measures are “Euclidean” and “1-corr”. |
avg.s |
a vector of average sihouette indices for the different partitions
in |
CH |
a vector of CH indices for the different partitions in |
Rand |
a matrix of Rand indices measuring the pair-wise agreement among
the different partitions in |
HA |
a matrix of Hubert and Arabie's adjusted Rand indices measuring
the pair-wise agreement among the different partitions in |
MA |
a matrix of Morey and Agresti's adjusted Rand indices measuring
the pair-wise agreement among the different partitions in |
FM |
a matrix of Fowlkes and Mallows's indices measuring
the pair-wise agreement among the different partitions in |
Jaccard |
a matrix of Jaccard indices measuring
the pair-wise agreement among the different partitions in |
Calinski, R.B., Harabasz, J., (1974). A dendrite method for cluster analysis. Communications in Statistics, Vol. 3, pages 1-27.
Kaufman, L., Rousseeuw, P.J., (1990). Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York.
Milligan, G.W. and Cooper, M.C. (1986) A study of the comparability of external criteria for hierarchical cluster analysis. Multivariate Behavioral Research 21, 441–458.
Wang, S., Qiu, W., and Zamar, R. H. (2007). CLUES: A non-parametric clustering method based on local shrinking. Computational Statistics & Data Analysis, Vol. 52, issue 1, pages 286-298.
# Maronna data set data(Maronna) # data matrix maronna <- Maronna$maronna # cluster membership maronna.mem <- Maronna$maronna.mem # partition by clues and kmeans res_CH <- clues(maronna, strengthMethod = "CH", quiet = TRUE) res_sil <- clues(maronna, strengthMethod = "sil", quiet = TRUE) res_km_HW <- kmeans(maronna, 4, algorithm = "Hartigan-Wong") res_km_L <- kmeans(maronna, 4, algorithm = "Lloyd") res_km_F <- kmeans(maronna, 4, algorithm = "Forgy") res_km_M <- kmeans(maronna, 4, algorithm = "MacQueen") memMat <- cbind(maronna.mem, res_CH$mem, res_sil$mem, res_km_HW$cluster, res_km_L$cluster, res_km_F$cluster, res_km_M$cluster) colnames(memMat) <- c("true", "clues_CH", "clues_sil", "km_HW", "km_L", "km_F", "km_M") res <- compClust(maronna, memMat) print(sapply(res, function(x) {round(x,1)}))