Cluster analysis in R: determine the optimal number of clusters

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Top 5 Answer for Cluster analysis in R: determine the optimal number of clusters

vote vote

90

If your question is how can I determine how many clusters are appropriate for a kmeans analysis of my data?, then here are some options. The wikipedia article on determining numbers of clusters has a good review of some of these methods.

First, some reproducible data (the data in the Q are... unclear to me):

n = 100 g = 6  set.seed(g) d <- data.frame(x = unlist(lapply(1:g, function(i) rnorm(n/g, runif(1)*i^2))),                  y = unlist(lapply(1:g, function(i) rnorm(n/g, runif(1)*i^2)))) plot(d) 

enter image description here

One. Look for a bend or elbow in the sum of squared error (SSE) scree plot. See http://www.statmethods.net/advstats/cluster.html & http://www.mattpeeples.net/kmeans.html for more. The location of the elbow in the resulting plot suggests a suitable number of clusters for the kmeans:

mydata <- d wss <- (nrow(mydata)-1)*sum(apply(mydata,2,var))   for (i in 2:15) wss[i] <- sum(kmeans(mydata,                                        centers=i)$withinss) plot(1:15, wss, type="b", xlab="Number of Clusters",      ylab="Within groups sum of squares") 

We might conclude that 4 clusters would be indicated by this method: enter image description here

Two. You can do partitioning around medoids to estimate the number of clusters using the pamk function in the fpc package.

library(fpc) pamk.best <- pamk(d) cat("number of clusters estimated by optimum average silhouette width:", pamk.best$nc, "\n") plot(pam(d, pamk.best$nc)) 

enter image description here enter image description here

# we could also do: library(fpc) asw <- numeric(20) for (k in 2:20)   asw[[k]] <- pam(d, k) $ silinfo $ avg.width k.best <- which.max(asw) cat("silhouette-optimal number of clusters:", k.best, "\n") # still 4 

Three. Calinsky criterion: Another approach to diagnosing how many clusters suit the data. In this case we try 1 to 10 groups.

require(vegan) fit <- cascadeKM(scale(d, center = TRUE,  scale = TRUE), 1, 10, iter = 1000) plot(fit, sortg = TRUE, grpmts.plot = TRUE) calinski.best <- as.numeric(which.max(fit$results[2,])) cat("Calinski criterion optimal number of clusters:", calinski.best, "\n") # 5 clusters! 

enter image description here

Four. Determine the optimal model and number of clusters according to the Bayesian Information Criterion for expectation-maximization, initialized by hierarchical clustering for parameterized Gaussian mixture models

# See http://www.jstatsoft.org/v18/i06/paper # http://www.stat.washington.edu/research/reports/2006/tr504.pdf # library(mclust) # Run the function to see how many clusters # it finds to be optimal, set it to search for # at least 1 model and up 20. d_clust <- Mclust(as.matrix(d), G=1:20) m.best <- dim(d_clust$z)[2] cat("model-based optimal number of clusters:", m.best, "\n") # 4 clusters plot(d_clust) 

enter image description here enter image description here enter image description here

Five. Affinity propagation (AP) clustering, see http://dx.doi.org/10.1126/science.1136800

library(apcluster) d.apclus <- apcluster(negDistMat(r=2), d) cat("affinity propogation optimal number of clusters:", length(d.apclus@clusters), "\n") # 4 heatmap(d.apclus) plot(d.apclus, d) 

enter image description here enter image description here

Six. Gap Statistic for Estimating the Number of Clusters. See also some code for a nice graphical output. Trying 2-10 clusters here:

library(cluster) clusGap(d, kmeans, 10, B = 100, verbose = interactive())  Clustering k = 1,2,..., K.max (= 10): .. done Bootstrapping, b = 1,2,..., B (= 100)  [one "." per sample]: .................................................. 50  .................................................. 100  Clustering Gap statistic ["clusGap"]. B=100 simulated reference sets, k = 1..10  --> Number of clusters (method 'firstSEmax', SE.factor=1): 4           logW   E.logW        gap     SE.sim  [1,] 5.991701 5.970454 -0.0212471 0.04388506  [2,] 5.152666 5.367256  0.2145907 0.04057451  [3,] 4.557779 5.069601  0.5118225 0.03215540  [4,] 3.928959 4.880453  0.9514943 0.04630399  [5,] 3.789319 4.766903  0.9775842 0.04826191  [6,] 3.747539 4.670100  0.9225607 0.03898850  [7,] 3.582373 4.590136  1.0077628 0.04892236  [8,] 3.528791 4.509247  0.9804556 0.04701930  [9,] 3.442481 4.433200  0.9907197 0.04935647 [10,] 3.445291 4.369232  0.9239414 0.05055486 

Here's the output from Edwin Chen's implementation of the gap statistic: enter image description here

Seven. You may also find it useful to explore your data with clustergrams to visualize cluster assignment, see http://www.r-statistics.com/2010/06/clustergram-visualization-and-diagnostics-for-cluster-analysis-r-code/ for more details.

Eight. The NbClust package provides 30 indices to determine the number of clusters in a dataset.

library(NbClust) nb <- NbClust(d, diss=NULL, distance = "euclidean",         method = "kmeans", min.nc=2, max.nc=15,          index = "alllong", alphaBeale = 0.1) hist(nb$Best.nc[1,], breaks = max(na.omit(nb$Best.nc[1,]))) # Looks like 3 is the most frequently determined number of clusters # and curiously, four clusters is not in the output at all! 

enter image description here

If your question is how can I produce a dendrogram to visualize the results of my cluster analysis, then you should start with these: http://www.statmethods.net/advstats/cluster.html http://www.r-tutor.com/gpu-computing/clustering/hierarchical-cluster-analysis http://gastonsanchez.wordpress.com/2012/10/03/7-ways-to-plot-dendrograms-in-r/ And see here for more exotic methods: http://cran.r-project.org/web/views/Cluster.html

Here are a few examples:

d_dist <- dist(as.matrix(d))   # find distance matrix  plot(hclust(d_dist))           # apply hirarchical clustering and plot 

enter image description here

# a Bayesian clustering method, good for high-dimension data, more details: # http://vahid.probstat.ca/paper/2012-bclust.pdf install.packages("bclust") library(bclust) x <- as.matrix(d) d.bclus <- bclust(x, transformed.par = c(0, -50, log(16), 0, 0, 0)) viplot(imp(d.bclus)$var); plot(d.bclus); ditplot(d.bclus) dptplot(d.bclus, scale = 20, horizbar.plot = TRUE,varimp = imp(d.bclus)$var, horizbar.distance = 0, dendrogram.lwd = 2) # I just include the dendrogram here 

enter image description here

Also for high-dimension data is the pvclust library which calculates p-values for hierarchical clustering via multiscale bootstrap resampling. Here's the example from the documentation (wont work on such low dimensional data as in my example):

library(pvclust) library(MASS) data(Boston) boston.pv <- pvclust(Boston) plot(boston.pv) 

enter image description here

Does any of that help?

vote vote

85

It's hard to add something too such an elaborate answer. Though I feel we should mention identify here, particularly because @Ben shows a lot of dendrogram examples.

d_dist <- dist(as.matrix(d))   # find distance matrix  plot(hclust(d_dist))  clusters <- identify(hclust(d_dist)) 

identify lets you interactively choose clusters from an dendrogram and stores your choices to a list. Hit Esc to leave interactive mode and return to R console. Note, that the list contains the indices, not the rownames (as opposed to cutree).

vote vote

75

In order to determine optimal k-cluster in clustering methods. I usually using Elbow method accompany by Parallel processing to avoid time-comsuming. This code can sample like this:

Elbow method

elbow.k <- function(mydata){ dist.obj <- dist(mydata) hclust.obj <- hclust(dist.obj) css.obj <- css.hclust(dist.obj,hclust.obj) elbow.obj <- elbow.batch(css.obj) k <- elbow.obj$k return(k) } 

Running Elbow parallel

no_cores <- detectCores()     cl<-makeCluster(no_cores)     clusterEvalQ(cl, library(GMD))     clusterExport(cl, list("data.clustering", "data.convert", "elbow.k", "clustering.kmeans"))  start.time <- Sys.time()  elbow.k.handle(data.clustering))  k.clusters <- parSapply(cl, 1, function(x) elbow.k(data.clustering))     end.time <- Sys.time()     cat('Time to find k using Elbow method is',(end.time - start.time),'seconds with k value:', k.clusters) 

It works well.

vote vote

60

A simple solution is the library factoextra. You can change the clustering method and the method for calculate the best number of groups. For example if you want to know the best number of clusters for a k- means:

Data: mtcars

library(factoextra)    fviz_nbclust(mtcars, kmeans, method = "wss") +       geom_vline(xintercept = 3, linetype = 2)+       labs(subtitle = "Elbow method") 

Finally, we get a graph like:

enter image description here

vote vote

54

Splendid answer from Ben. However I'm surprised that the Affinity Propagation (AP) method has been here suggested just to find the number of cluster for the k-means method, where in general AP do a better job clustering the data. Please see the scientific paper supporting this method in Science here:

Frey, Brendan J., and Delbert Dueck. "Clustering by passing messages between data points." science 315.5814 (2007): 972-976.

So if you are not biased toward k-means I suggest to use AP directly, which will cluster the data without requiring knowing the number of clusters:

library(apcluster) apclus = apcluster(negDistMat(r=2), data) show(apclus) 

If negative euclidean distances are not appropriate, then you can use another similarity measures provided in the same package. For example, for similarities based on Spearman correlations, this is what you need:

sim = corSimMat(data, method="spearman") apclus = apcluster(s=sim) 

Please note that those functions for similarities in the AP package are just provided for simplicity. In fact, apcluster() function in R will accept any matrix of correlations. The same before with corSimMat() can be done with this:

sim = cor(data, method="spearman") 

or

sim = cor(t(data), method="spearman") 

depending on what you want to cluster on your matrix (rows or cols).

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