kmpart

K-means partition of points

R

kmpart(
  x,
  y = NULL,
  k,
  init = "pp",
  cell = NULL,
  upd = "mean",
  maxit = 100,
  seed = NULL,
  count = NULL,
  lonlat = FALSE
)

Partitions the points into k groups by Lloyd’s iterations: each point joins its nearest centre (the lowest-numbered on ties), then each centre moves to its points’ mean (upd = "mean", K-means, minimising the within-group sum of squares) or to their centre of minimum distance (upd = "weber", a spatial K-medians minimising the sum of distances), until no point changes group or after maxit moves. An emptied group keeps its centre. The result depends on the start: k-means++ seeding (Arthur and Vassilvitskii 2007), the centres of the busiest grid cells at least a given distance apart, or centres given.

Parameters

x, y

The points: x and y numeric vectors of equal length; or x a matrix or data frame with columns named x and y (or X and Y, as sf::st_coordinates() names them, or lon and lat with lonlat = TRUE) and y NULL; or x an sf or sfc object of POINT geometries, whose coordinate reference system must agree with lonlat. An unnamed two-column matrix is read as x then y; other columns are never taken by position. Vectors given separately (x, y, and w or t where a function takes them) are matched by name when every one is named and no name repeats, as elsewhere in the package; otherwise by position. No missing or infinite values.

k

The number of groups: one whole number from 1 to the number of points.

init

The start: "pp" (k-means++, drawn from seed), "cells" (square cells of side cell[1] from the lower-left corner of the points’ bounding box, taken by decreasing count, a cell’s centre becoming a seed when it is at least cell[2] from every earlier one), or the k starting centres as a matrix or data frame of coordinates (degrees when lonlat = TRUE).

cell

For init = "cells": c(side, separation), the side positive and the separation from 0, in the unit of the coordinates.

upd

The centre update: "mean" or "weber".

maxit

The largest number of iterations: one whole number from 0.

seed

NULL to draw the simulations’ seed from R’s generator (so set.seed() fixes them), or one whole number from 0.

count

NULL for points, or for zones: one whole count from 0 per zone, the points x, y being the zones’ centroids. A zone is taken as count incidents at its centroid, which these hot-spot rules treat exactly as coincident points. Zones with count 0 get NA.

lonlat

FALSE (the default) when x and y are planar coordinates in one length unit; TRUE when they are longitude and latitude in degrees, which are then projected to metres by eqproj() about their own centre, and centres are returned in degrees. It is never guessed.

Returns

A list. cl, the group of each point (1 to k, input order). cen, a data frame with one row per group: x, y (its centre, in degrees when lonlat = TRUE), n (points), ss (sum of squared distances to the centre) and sd (sum of distances). fit, a named vector: ss and sd (totals), iter (moves made) and conv (1 if no point changed group at the end).

References

Lloyd, S. (1982). Least squares quantization in PCM. IEEE Transactions on Information Theory, 28(2), 129-137. doi:10.1109/TIT.1982.1056489

Arthur, D. and Vassilvitskii, S. (2007). k-means++: the advantages of careful seeding. Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1027-1035.

Examples

set.seed(1)
x <- c(rnorm(30, 0), rnorm(30, 5))
y <- c(rnorm(30, 0), rnorm(30, 5))
kmpart(x, y, k = 2, seed = 1)$cen

Generated from the R help page: kmpart in the R reference.