Solved – Variables involved in kNNdistplot (dbscan package) in R

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I have a time-series of a feature(metric) for 4 different servers each of length 2000. I want to use dbscan algorithm to figure out if all 4 machines fall in the same cluster or not using dbcscan on these 4 time-series.

I am using the dbscan package in R and my input is a 4 x 2000 matrix(inputMatrix) to the dbscan function. To determine the parameters I am determining the value of k/minpts as follows.

Calculation of k:
1.) There are 2000 points and 4 rows. Considering one column at a time, I am calculating the distance of each point from the remaining three points and then taking the mean. So this gives me 4 avg distances corresponding to 4 servers/rows at a particular time.
So I again have a 4 x 2000 matrix of distances(distMatrix).

distmat<-function(x){ #each column of distance is the distances of each server with other servers. distance<-as.matrix(dist(x = x,method = "euclidean",diag=T,upper=T)) return(apply(X = distance,MARGIN = 1,FUN = mean)) }  distMatrix<-apply(X = inputMatrix,MARGIN = 2,FUN = distmat)

2.) With each point as a center in the inputMatrix and corresponding avg dist in distMatrix as radius I calculated the maximum number of points that lie in the neighbourhood.

numberofpoints<-matrix(data = rep(x = 0,8000),nrow = 4,ncol = 2000) for(i in 1:ncol(inputMatrix)){     for(j in 1:nrow(inputMatrix)){         numberofpoints[j,i]=length(which(inputMatrix[,i]<=inputMatrix[j,i]+distMatrix[j,i] & inputMatrix[,i]>=inputMatrix[j,i]-distMatrix[j,i]))     } }

Again taking a mean over the column first and then over the row yields the value of k/minpts.

meannumberofpoints<-apply(X = numberofpoints,MARGIN = 2,FUN = mean) k=mean(meannumberofpoints)

k for my data is 2.167125

To find EPS: There is an inbuilt kNNdistplot function in dbscan package in R which plots the knee-like graph.

kNNdistplot

The horizontal line across the image corresponds to the eps value.
However, I am not sure what variables it is plotting on the two axes. I want to automate this sorted k-graph calculation and plot it but I am not sure where to start.

Can anyone please explain what are the variables/values plotted on the x and y axis and how to calculate these.
Thanks.

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Best Answer

Something is very messed up here.

The usual approach would be to consider the four servers to be four "points". But at data this tiny DBSCAN does not make sense!

I'd suggest to use a time series distance function, and hierarchical clustering.

It appear that your approach is to treat the data as 2000 data sets, each with 4 points with 1 attribute each. But what magic do you expect DBSCAN to do there? And how did you manage ro end up with a non-integer k? What is the 2.12345 nearest neighbor supposed to be?!?

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