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Generate initial cluster assignments

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

Creates an undirected graph from spatial data or a weighted adjacency matrix, computes its minimum spanning tree (MST), and partitions it into nclust clusters. Accepts weighted matrix or Matrix objects, and stars objects with either vector geometry (contiguity via sf::st_touches()) or raster dimensions (4-connected grid adjacency for non-NA pixels).

Usage

genclust(x, ...)

# Default S3 method
genclust(x, ...)

# S3 method for class 'matrix'
genclust(x, nclust = 10, weights = NULL, ...)

# S3 method for class 'Matrix'
genclust(x, nclust = 10, weights = NULL, ...)

# S3 method for class 'stars'
genclust(x, nclust = 10, spnames = NULL, response = NULL, weights = NULL, ...)

Arguments

x

Spatial data or adjacency matrix. Accepted classes: matrix, Matrix, or stars.

...

Not used; required for S3 method consistency.

nclust

Integer. Number of initial clusters (default 10).

weights

Optional numeric vector of edge weights with n^2 elements, where n is the total number of spatial units (before filtering). If NULL, random weights are assigned.

spnames

Character vector with the names of the spatial dimensions. If NULL, auto-detected as dimensions with a non-NA regular delta in stars::st_dimensions(). Currently supports 1D (vector geometry) and 2D raster grids; 3D spatial grids (e.g. x, y, z) are not yet supported.

response

Character. Name of the attribute in x to use for determining valid spatial cells (cells where all observations are NA are excluded). If NULL (default), all spatial cells are treated as valid.

Value

A list with:

  • graph: undirected igraph object representing spatial contiguity.

  • mst: minimum spanning tree of graph.

  • membership: integer vector of cluster assignments (length = number of valid spatial units).

  • valid_ids: integer vector of flat spatial positions included in the graph (only present for stars input; NULL for matrix/Matrix input).

Examples


library(sfclust)
library(sf)
library(stars)

# stars object with vector geometry
geom <- st_make_grid(cellsize = c(1, 1), offset = c(0, 0), n = c(3, 2))
x <- st_as_stars(st_sf(z = 1:6, geometry = geom))
clust <- genclust(x, nclust = 3)
plot(st_sf(geom, cluster = factor(clust$membership)))


# stars raster input
x <- st_as_stars(cluster = matrix(1:35, 5))
clust <- genclust(x, nclust = 4)
x$cluster <- clust$membership
plot(x, col = rainbow(4))


# matrix input
x <- matrix(c(0,1,0,1, 1,0,1,0, 0,1,0,1, 1,0,1,0), nrow = 4)
clust <- genclust(x, nclust = 2)
clust$membership
#> [1] 1 2 1 1