K-Medoids in R: Step-by-Step Example


Clustering is a technique in machine learning that attempts to find groups or clusters of observations within a dataset.

The goal is to find clusters such that the observations within each cluster are quite similar to each other, while observations in different clusters are quite different from each other.

Clustering is a form of unsupervised learning because we’re simply attempting to find structure within a dataset rather than predicting the value of some response variable.

Clustering is often used in marketing when companies have access to information like:

  • Household income
  • Household size
  • Head of household Occupation
  • Distance from nearest urban area

When this information is available, clustering can be used to identify households that are similar and may be more likely to purchase certain products or respond better to a certain type of advertising.

One of the most common forms of clustering is known as k-means clustering.

Unfortunately, this method can be influenced by outliers so an alternative that is often used is k-medoids clustering.

What is K-Medoids Clustering?

K-medoids clustering is a technique in which we place each observation in a dataset into one of K clusters.

The end goal is to have clusters in which the observations within each cluster are quite similar to each other while the observations in different clusters are quite different from each other.

In practice, we use the following steps to perform K-means clustering:

1. Choose a value for K.

  • First, we must decide how many clusters we’d like to identify in the data. Often we have to simply test several different values for K and analyze the results to see which number of clusters seems to make the most sense for a given problem.

2. Randomly assign each observation to an initial cluster, from 1 to K.

3. Perform the following procedure until the cluster assignments stop changing.

  • For each of the clusters, compute the cluster centroid. This is the vector of the p feature medians for the observations in the kth cluster.
  • Assign each observation to the cluster whose centroid is closest. Here, closest is defined using Euclidean distance.

Technical Note:

 

Because k-medoids computes cluster centroids using medians instead of means, it tends to be more robust to outliers compared to k-means.

 

In practice, if there are no extreme outliers in the dataset then k-means and k-medoids will produce similar results.

K-Medoids Clustering in R

The following tutorial provides a step-by-step example of how to perform k-medoids clustering in R.

Step 1: Load the Necessary Packages

First, we’ll load two packages that contain several useful functions for k-medoids clustering in R.

library(factoextra)
library(cluster)

Step 2: Load and Prep the Data

For this example we’ll use the USArrests dataset built into R, which contains the number of arrests per 100,000 residents in each U.S. state in 1973 for Murder, Assault, and Rape along with the percentage of the population in each state living in urban areas, UrbanPop.

The following code shows how to do the following:

  • Load the USArrests dataset
  • Remove any rows with missing values
  • Scale each variable in the dataset to have a mean of 0 and a standard deviation of 1
#load data
df <- USArrests

#remove rows with missing values
df <- na.omit(df)

#scale each variable to have a mean of 0 and sd of 1
df <- scale(df)

#view first six rows of dataset
head(df)

               Murder   Assault   UrbanPop         Rape
Alabama    1.24256408 0.7828393 -0.5209066 -0.003416473
Alaska     0.50786248 1.1068225 -1.2117642  2.484202941
Arizona    0.07163341 1.4788032  0.9989801  1.042878388
Arkansas   0.23234938 0.2308680 -1.0735927 -0.184916602
California 0.27826823 1.2628144  1.7589234  2.067820292
Colorado   0.02571456 0.3988593  0.8608085  1.864967207

Step 3: Find the Optimal Number of Clusters

To perform k-medoids clustering in R we can use the pam() function, which stands for “partitioning around medians” and uses the following syntax:

pam(data, k, metric = “euclidean”, stand = FALSE)

where:

  • data: Name of the dataset.
  • k: The number of clusters.
  • metric: The metric to use to calculate distance. Default is euclidean but you could also specify manhattan.
  • stand: Whether or not to standardize each variable in the dataset. Default is FALSE.

Since we don’t know beforehand how many clusters is optimal, we’ll create two different plots that can help us decide:

1. Number of Clusters vs. the Total Within Sum of Squares

First, we’ll use the fviz_nbclust() function to create a plot of the number of clusters vs. the total within sum of squares:

fviz_nbclust(df, pam, method = "wss")

Optimal clusters for k-medoids

The total within sum of squares will typically always increase as we increase the number of clusters, so when we create this type of plot we look for an “elbow” where the sum of squares begins to “bend” or level off.

The point where the plot bends is typically the optimal number of clusters. Beyond this number, overfitting is likely to occur.

For this plot it appear that there is a bit of an elbow or “bend” at k = 4 clusters.

2. Number of Clusters vs. Gap Statistic

Another way to determine the optimal number of clusters is to use a metric known as the gap statistic, which compares the total intra-cluster variation for different values of k with their expected values for a distribution with no clustering.

We can calculate the gap statistic for each number of clusters using the clusGap() function from the cluster package along with a plot of clusters vs. gap statistic using the fviz_gap_stat() function:

#calculate gap statistic based on number of clusters
gap_stat <- clusGap(df,
                    FUN = pam,
                    K.max = 10, #max clusters to consider
                    B = 50) #total bootstrapped iterations

#plot number of clusters vs. gap statistic
fviz_gap_stat(gap_stat)

K-medoids optimal number of clusters in R

From the plot we can see that gap statistic is highest at k = 4 clusters, which matches the elbow method we used earlier.

Step 4: Perform K-Medoids Clustering with Optimal K

Lastly, we can perform k-medoids clustering on the dataset using the optimal value for k of 4:

#make this example reproducible
set.seed(1)

#perform k-medoids clustering with k = 4 clusters
kmed <- pam(df, k = 4)

#view results
kmed

              ID     Murder    Assault   UrbanPop         Rape
Alabama        1  1.2425641  0.7828393 -0.5209066 -0.003416473
Michigan      22  0.9900104  1.0108275  0.5844655  1.480613993
Oklahoma      36 -0.2727580 -0.2371077  0.1699510 -0.131534211
New Hampshire 29 -1.3059321 -1.3650491 -0.6590781 -1.252564419
Clustering vector:
       Alabama         Alaska        Arizona       Arkansas     California 
             1              2              2              1              2 
      Colorado    Connecticut       Delaware        Florida        Georgia 
             2              3              3              2              1 
        Hawaii          Idaho       Illinois        Indiana           Iowa 
             3              4              2              3              4 
        Kansas       Kentucky      Louisiana          Maine       Maryland 
             3              3              1              4              2 
 Massachusetts       Michigan      Minnesota    Mississippi       Missouri 
             3              2              4              1              3 
       Montana       Nebraska         Nevada  New Hampshire     New Jersey 
             3              3              2              4              3 
    New Mexico       New York North Carolina   North Dakota           Ohio 
             2              2              1              4              3 
      Oklahoma         Oregon   Pennsylvania   Rhode Island South Carolina 
             3              3              3              3              1 
  South Dakota      Tennessee          Texas           Utah        Vermont 
             4              1              2              3              4 
      Virginia     Washington  West Virginia      Wisconsin        Wyoming 
             3              3              4              4              3 
Objective function:
   build     swap 
1.035116 1.027102 

Available components:
 [1] "medoids"    "id.med"     "clustering" "objective"  "isolation" 
 [6] "clusinfo"   "silinfo"    "diss"       "call"       "data"          

Note that the four cluster centroids are actual observations in the dataset. Near the top of the output we can see that the four centroids are the following states:

  • Alabama
  • Michigan
  • Oklahoma
  • New Hampshire

We can visualize the clusters on a scatterplot that displays the first two principal components on the axes using the fivz_cluster() function:

#plot results of final k-medoids model
fviz_cluster(kmed, data = df)

Plot k-medoids clusters in R

We can also append the cluster assignments of each state back to the original dataset:

#add cluster assignment to original data
final_data <- cbind(USArrests, cluster = kmed$cluster)

#view final data
head(final_data)

           Murder Assault UrbanPop Rape cluster
Alabama      13.2     236       58 21.2       1
Alaska       10.0     263       48 44.5       2
Arizona       8.1     294       80 31.0       2
Arkansas      8.8     190       50 19.5       1
California    9.0     276       91 40.6       2
Colorado      7.9     204       78 38.7       2

You can find the complete R code used in this example here.

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