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Generate clusters for spatial clustering

Source: R/generate-clusters.R
genclust.Rd

Creates an undirected graph from spatial polygonal data, computes its minimum spanning tree (MST), and generates nclust clusters. This function is used to initialize cluster membership in a clustering algorithm, such as sfclust.

Usage

genclust(x, nclust = 10, weights = NULL)

Arguments

x

An sf or sfc object representing spatial polygonal data. It can also be a matrix or Matrix object with non-zero values representing weighted connectivity between units.

nclust

Integer, specifying the initial number of clusters.

weights

Optional numeric vector or matrix of weights between units in x. It should have dimensions n^2, where n is the number of units in x. If NULL, random weights are assigned.

Value

A list with three elements:

  • graph: The undirected graph object representing spatial contiguity.

  • mst: The minimum spanning tree.

  • membership: The cluster membership for elements in x.

Examples


library(sfclust)
library(sf)

x <- st_make_grid(cellsize = c(1, 1), offset = c(0, 0), n = c(3, 2))

# using distance between geometries
clust <- genclust(x, nclust = 3, weights = st_distance(st_centroid(x)))
print(clust)
#> $graph
#> IGRAPH 57acc5a UNW- 6 11 -- 
#> + attr: name (v/c), weight (e/n)
#> + edges from 57acc5a (vertex names):
#>  [1] 1--2 1--4 1--5 2--3 2--4 2--5 2--6 3--5 3--6 4--5 5--6
#> 
#> $mst
#> IGRAPH 6ea8a4c UNW- 6 5 -- 
#> + attr: name (v/c), vid (v/n), weight (e/n)
#> + edges from 6ea8a4c (vertex names):
#> [1] 1--4 2--3 3--6 4--5 5--6
#> 
#> $membership
#> 1 2 3 4 5 6 
#> 1 2 3 3 3 3 
#> 
plot(st_sf(x, cluster = factor(clust$membership)))


# using increasing weights
cluster_ini <- genclust(x, nclust = 3, weights = 1:36)
print(cluster_ini)
#> $graph
#> IGRAPH 70782be U-W- 6 11 -- 
#> + attr: weight (e/n)
#> + edges from 70782be:
#>  [1] 1--2 1--4 1--5 2--3 2--4 2--5 2--6 3--5 3--6 4--5 5--6
#> 
#> $mst
#> IGRAPH 2d96e13 U-W- 6 5 -- 
#> + attr: vid (v/n), weight (e/n)
#> + edges from 2d96e13:
#> [1] 1--2 1--4 1--5 2--3 2--6
#> 
#> $membership
#> [1] 1 1 1 1 2 3
#> 
plot(st_sf(x, cluster = factor(cluster_ini$membership)))


# using on random weights
cluster_ini <- genclust(x, nclust = 3, weights = runif(36))
print(cluster_ini)
#> $graph
#> IGRAPH 77a0fbd U-W- 6 11 -- 
#> + attr: weight (e/n)
#> + edges from 77a0fbd:
#>  [1] 1--2 1--4 1--5 2--3 2--4 2--5 2--6 3--5 3--6 4--5 5--6
#> 
#> $mst
#> IGRAPH be76d77 U-W- 6 5 -- 
#> + attr: vid (v/n), weight (e/n)
#> + edges from be76d77:
#> [1] 1--4 2--4 2--6 3--5 3--6
#> 
#> $membership
#> [1] 1 2 3 1 3 3
#> 
plot(st_sf(x, cluster = factor(cluster_ini$membership)))