How to Calculate Hamming Distance in R

In data analysis and machine learning, it’s often necessary to quantify the difference between pairs of data points. When these data points are represented as strings or vectors, one of the most common measures of difference is the Hamming distance. Named after Richard Hamming, an American mathematician and computer scientist, the Hamming distance between two strings of equal length is the number of positions at which the corresponding symbols differ.

In this article, we will delve into the concept of Hamming distance and how you can calculate it in R. We’ll cover the basics of Hamming distance, and then proceed with a comprehensive guide on how to compute Hamming distance using base R functions and dedicated packages.

Understanding Hamming Distance

Hamming distance is used to measure the minimum number of substitutions required to change one string into the other or, in other words, the minimum number of errors that could have transformed one string into the other.

Given two strings of equal length, the Hamming distance is the number of positions at which the corresponding values are different. For example, the Hamming distance between the strings “karolin” and “kathrin” is 3 because they differ in three positions:

karolin
kathrin

Base R Method to Calculate Hamming Distance

To compute Hamming distance using R’s base functions, we can create a custom function. This function will compare each element in the input vectors, sum up the number of differences, and return the result.

Here’s how you can define the function and calculate the Hamming distance:

# Define vectors
vector1 <- c(1, 0, 0, 1, 1)
vector2 <- c(0, 1, 0, 1, 0)

# Define Hamming distance function
hamming_distance <- function(v1, v2) {
  sum(v1 != v2)
}

# Calculate Hamming distance
distance <- hamming_distance(vector1, vector2)
print(distance)

In the hamming_distance function, the != operator compares each corresponding pair of elements in the vectors and returns TRUE if they are not equal and FALSE if they are equal. The sum function then adds up the number of TRUE values, which is the Hamming distance.

Using the stringdist Package

When working with strings, the stringdist package provides a convenient way to calculate the Hamming distance. Let’s calculate the Hamming distance between the strings “karolin” and “kathrin”:

# Install the stringdist package
if (!"stringdist" %in% rownames(installed.packages())) {install.packages("stringdist")}

# Load the stringdist package
library(stringdist)

# Define strings
string1 <- "karolin"
string2 <- "kathrin"

# Calculate Hamming distance
distance <- stringdist::stringdist(string1, string2, method = "hamming")
print(distance)

In this code, the stringdist function from the stringdist package calculates the Hamming distance between string1 and string2 using the “hamming” method.

Conclusion

The Hamming distance is a simple yet powerful concept, particularly useful when you need to compare the similarity between two strings or binary vectors. This article has provided you with comprehensive steps on how to calculate the Hamming distance using R.