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K-means is efficient, and perhaps, the most popular clustering method. It is a way for finding natural groups in otherwise unlabeled data. You specify the number of clusters you want defined and the algorithm minimizes the total within-cluster variance.

In this exercise, we will play around with the base R inbuilt k-means function on some labeled data.

Solutions are available here.

Exercise 1

Feed the columns with sepal measurements in the inbuilt iris data-set to the k-means; save the cluster vector of each observation. Use 3 centers and set the random seed to 1 before.

Exercise 2

Check the proportions of each species by cluster.

Exercise 3

Make a plot with sepal length on the horizontal axis and width on the vertical axis. Find a way to visualize both the actual species and the cluster the algorithm is categorized into.

Exercise 4

Repeat the clustering from step one, but include petal measurements also. Does the clustering reflect the actual species better now?

Learn more about cluster analysis in the online course Applied Multivariate Analysis with R. In this course you will learn how to work with hiërarchical clustering, k-means clustering and much more.

Exercise 5

Create a new data-set identical to iris, but multiply the “Petal.Width” by 2. Are the results different now?

Exercise 6

Standardize your new data-set so that each variable has a mean of 0 and a variance of 1; check once more if multiplying by two makes a difference.

Exercise 7

Read in the Titanic train.csv data-set from Kaggle.com (you might have to sign up first). Turn the sex column into a dummy variable, =1, if it is male, “0” otherwise, and “Pclass” into a dummy variable for the most common class 3. Using four columns, Sex, SibSp, Parch and Fare, apply the k-means algorithm to get 4 clusters and use nstart=20. Remember to set the seed to 1 so the results are comparable. Note that these four variables have no special meaning to the problem and dummy data in k-means is probably not a good idea in general – we are just playing around.

Exercise 8

Now, how would you describe, in words, each of the clusters and what the survival rates were?

Exercise 9

Now, 4 clusters was an arbitrary choice. Apply k-means clustering using nstart=20, but using k from 2 to 20 and store the result.

Exercise 10

Plot the percent of variance explained by the clusters (between sum of squares over the total sum of squares). What seems like a reasonable number of clusters, according to the elbow method?

(Picture by giveawayboy)