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R cluster package for clustering algorithms. Use for PAM, CLARA, AGNES, DIANA, and other clustering methods.
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| name | cluster |
| description | R cluster package for clustering algorithms. Use for PAM, CLARA, AGNES, DIANA, and other clustering methods. |
Finding groups in data.
library(cluster)
# PAM clustering
pam_result <- pam(data, k = 3)
# Results
pam_result$clustering # Cluster assignments
pam_result$medoids # Medoid points
pam_result$silinfo # Silhouette info
# Plot
plot(pam_result)
# CLARA for large datasets
clara_result <- clara(data, k = 3, samples = 50)
# Results
clara_result$clustering
clara_result$medoids
# Agglomerative (AGNES)
agnes_result <- agnes(data, method = "ward")
plot(agnes_result)
cutree(agnes_result, k = 3)
# Divisive (DIANA)
diana_result <- diana(data)
plot(diana_result)
cutree(diana_result, k = 3)
# Fuzzy c-means
fanny_result <- fanny(data, k = 3)
# Membership matrix
fanny_result$membership
# Hard clustering
fanny_result$clustering
# Compute silhouette
sil <- silhouette(clustering, dist(data))
# Summary
summary(sil)
# Plot
plot(sil)
# Average silhouette width
mean(sil[, 3])
# Compute distances
d <- daisy(data)
# Mixed data types
d <- daisy(data, metric = "gower")
# With weights
d <- daisy(data, weights = c(1, 2, 1))
# Gap statistic
gap_stat <- clusGap(data, FUN = pam, K.max = 10, B = 50)
plot(gap_stat)
# Optimal k
maxSE(gap_stat$Tab[, "gap"], gap_stat$Tab[, "SE.sim"])
# Cluster plot
clusplot(data, clustering,
color = TRUE,
shade = TRUE,
labels = 2,
lines = 0)