Saturday, November 3, 2018

Distance Matrix Example in R (Euclidean)

As some of you may hard to find a good example of distance matrix example in R with its explanation, I try to fill the gap with this article. Hope you will find it useful.

We use dist function in R to calculate distance matrix, with Euclidean distance as its default method.

As you recall, the Euclidean distance formula of two dimensional space between two points is:

    sqrt( (x2-x1)^2 + (y2-y1)^2 )

The distance formula of three dimensional space between two points is:

    sqrt( (x2-x1)^2 + (y2-y1)^2 + (z2 - z1)^2 )

Now, let's practice with its implementation in R. Along the example, we will use data frame variable named datatocalculate.

    > datatocalculate <- data.frame( x = c(1, 2), y = c(2, 4) )

    > datatocalculate
      x y
    1 1 2
    2 2 4

Now, let's calculate the distance matrix.

    > dist(datatocalculate)

The output should be like the following - with additional colors added to make it easy to explain later.

             1
    2 2.236068

The calculated distance from 1 to 2 is 2.236068. It is a result of the following calculation.

    sqrt((2-1)^2 + (4-2)^2)
    sqrt(5)
    2.236068

We will now modify datatocalculate with the following new values.

   > datatocalculate <- data.frame( x = c(1, 2, 1), y = c(2, 4, 6) )

   datatocalculate
     x y
   1 1 2
   2 2 4
   3 1 6

Calculate the distance matrix again.

   > dist(datatocalculate)
             1        2
    2 2.236068         
    3 4.000000 2.236068

The calculated distance from 1 to 2 is 2.236068. It is a result of the following calculation:

    sqrt((2-1)^2 + (4-2)^2)
    sqrt(5)
    2.236068

The calculated distance from 1 to 3 is 4.000000. It is a result of the following calculation:

    sqrt((1-1)^2 + (6-2)^2)
    sqrt(16)
    4.000000

The calculated distance from 2 to 3 is 2.236068. It is a result of the following calculation:

    sqrt((1-2)^2 + (6-4)^2)
    sqrt(5)
    2.236068

That's all. Hope this short article will make you clear on the usage of dist function in R.

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