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rderivativedbscan

How to select the second derivative greater than 1 in r

I'm looking for the exact value of epsilon to run the DBSCAN clustering algorithm.

Here's the KNN distance plot.

KNN distplot

This chart has two flex points. I need the second flex point. I'm using the following code:

# evaluate kNN distance
dist <- dbscan::kNNdist(iris, 4)

# order result
dist <- dist[order(dist)]

# scale
dist <- dist / max(dist)

# derivative
ddist <- diff(dist) / ( 1 / length(dist))

# get first point where derivative is higher than 1
knee <- dist[length(ddist)- length(ddist[ddist > 1])]

How can improve my code to get second point where derivative is higher than 1?

Solution

  • Sorry, can't reproduce your code (perhaps because of package version conflict), but it seems that which function would help you to find all positions, where ddist > 1: which(ddist > 1)