dbscan: pointdensity – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

pointdensity

Calculate Local Density at Each Data Point

Description

Calculate the local density at each data point as either the number of points in the eps-neighborhood (as used in dbscan()) or perform kernel density estimation (KDE) using a uniform kernel. The function uses a kd-tree for fast fixed-radius nearest neighbor search.

Usage

pointdensity(
  x,
  eps,
  type = "frequency",
  search = "kdtree",
  bucketSize = 10,
  splitRule = "suggest",
  approx = 0
)

Arguments

`x`	a data matrix.
`eps`	radius of the eps-neighborhood, i.e., bandwidth of the uniform kernel).
`type`	`"frequency"` or `"density"`. should the raw count of points inside the eps-neighborhood or the kde be returned.
`search, bucketSize, splitRule, approx`	algorithmic parameters for `frNN()`.

Details

dbscan() estimates the density around a point as the number of points in the eps-neighborhood of the point (including the query point itself). Kernel density estimation (KDE) using a uniform kernel, which is just this point count in the eps-neighborhood divided by (2 eps n), where n is the number of points in x.

Points with low local density often indicate noise (see e.g., Wishart (1969) and Hartigan (1975)).

Value

A vector of the same length as data points (rows) in x with the count or density values for each data point.

Author(s)

Michael Hahsler

References

Wishart, D. (1969), Mode Analysis: A Generalization of Nearest Neighbor which Reduces Chaining Effects, in Numerical Taxonomy, Ed., A.J. Cole, Academic Press, 282-311.

John A. Hartigan (1975), Clustering Algorithms, John Wiley & Sons, Inc., New York, NY, USA.

Examples

set.seed(665544)
n <- 100
x <- cbind(
  x=runif(10, 0, 5) + rnorm(n, sd = 0.4),
  y=runif(10, 0, 5) + rnorm(n, sd = 0.4)
  )
plot(x)

### calculate density
d <- pointdensity(x, eps = .5, type = "density")

### density distribution
summary(d)
hist(d, breaks = 10)

### plot with point size is proportional to Density
plot(x, pch = 19, main = "Density (eps = .5)", cex = d*5)

### Wishart (1969) single link clustering after removing low-density noise
# 1. remove noise with low density
f <- pointdensity(x, eps = .5, type = "frequency")
x_nonoise <- x[f >= 5,]

# 2. use single-linkage on the non-noise points
hc <- hclust(dist(x_nonoise), method = "single")
plot(x, pch = 19, cex = .5)
points(x_nonoise, pch = 19, col= cutree(hc, k = 4) + 1L)

dbscan

Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms

v1.1-10

GPL (>= 2)

Authors

Michael Hahsler [aut, cre, cph], Matthew Piekenbrock [aut, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]

Initial release

2022-01-14