# Introduction to k-Means clustering in R

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k-means clustering aims to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean, serving as a prototype of the cluster. I have provided below the R code to get started with k-means clustering in R. The dataset can be downloaded from here.

# Topics Covered # # 1. Reading data and Summary Statistics # 2. Determining the Optimal Number of Clusters # 3. Running Clustering Algorithm and Visualisations ############################################################################## #Reading data and Summary Statistics #change the working directory setwd("C:\\Users\\ujjwal.karn\\Desktop\\Classification & Clustering") mydata<-read.csv("data/kmeans_data.csv") head(mydata) str(mydata) summary(mydata) plot(mydata[c("Sepal.Length", "Sepal.Width")], main="Raw Data") #standardising the data mydata <- scale(mydata) ############################################################################## #Determining the Optimal Number of Clusters #http://stackoverflow.com/questions/15376075/cluster-analysis-in-r-determine-the-optimal-number-of-clusters/ wss <- (nrow(mydata)-1)*sum(apply(mydata,2,var)) for(i in 1:25){wss[i] <- sum(kmeans(mydata, centers=i)$withinss)} plot(1:25, wss, type="b", xlab="No. of Clusters", ylab="wss") wss ############################################################################## #Running Clustering Algorithm # trying with 4 clusters clus4 <- kmeans(mydata, centers=4, nstart=30) #check between_SS / total_SS clus4 # get cluster means aggregate(mydata ,by=list(clus4$cluster), FUN=mean) # append cluster assignment mydata <- data.frame(mydata, clus4$cluster) #summary groups <- data.frame(clus4$cluster) table(groups) plot(mydata[c("Sepal.Length", "Sepal.Width")], col=clus4$cluster) points(clus4$centers[,c("Sepal.Length", "Sepal.Width")], col=1:3, pch=8, cex=2) # trying with 3 clusters clus3 <- kmeans(mydata, centers=3, nstart=20) clus3 # get cluster means aggregate(mydata ,by=list(clus3$cluster), FUN=mean) # append cluster assignment mydata <- data.frame(mydata, clus3$cluster) #summary groups <- data.frame(clus3$cluster) table(groups) plot(mydata[c("Sepal.Length", "Sepal.Width")], col=clus3$cluster) points(clus3$centers[,c("Sepal.Length", "Sepal.Width")], col=1:3, pch=8, cex=2)

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