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Cluster Quality Metrics

Source: R/cluster-metrics.R
cluster_quality.Rd

Computes per-cluster and global quality metrics for network partitioning. Supports both binary and weighted networks.

Usage

cluster_quality(x, clusters, weighted = TRUE, directed = TRUE)

cqual(x, clusters, weighted = TRUE, directed = TRUE)

Arguments

x

Adjacency matrix (numeric)

clusters

Cluster specification (named list, data frame, or membership vector; see csum)

weighted

Logical; if TRUE (default), use edge weights; if FALSE, binarize the matrix first

directed

Logical; if TRUE (default), treat as directed network

Value

A cluster_quality object (a list) with:

per_cluster

Data frame, one row per cluster, with columns cluster (index), cluster_name, n_nodes, internal_edges (within-cluster weight), cut_edges (boundary-crossing weight), internal_density, avg_internal_degree, expansion, cut_ratio and conductance.

global

List with modularity (Newman-Girvan, computed on the weighted or binarized matrix), coverage (share of total weight that is internal to some cluster) and n_clusters.

See cluster_quality.

Examples

mat <- matrix(runif(100), 10, 10)
diag(mat) <- 0
clusters <- c(1,1,1,2,2,2,3,3,3,3)

q <- cluster_quality(mat, clusters)
q$per_cluster   # Per-cluster metrics
#>   cluster cluster_name n_nodes internal_edges cut_edges internal_density
#> 1       1            1       3       3.786687  21.06550        0.6311144
#> 2       2            2       3       2.859344  21.89879        0.4765574
#> 3       3            3       4       6.569519  24.70585        0.5474599
#>   avg_internal_degree expansion cut_ratio conductance
#> 1            2.524458  7.021834  1.003119   0.7355562
#> 2            1.906229  7.299596  1.042799   0.7929323
#> 3            3.284760  6.176463  1.029411   0.6528187
q$global        # Modularity, coverage
#> $modularity
#> [1] -0.05841018
#> 
#> $coverage
#> [1] 0.2808794
#> 
#> $n_clusters
#> [1] 3
#> 
mat <- matrix(runif(100), 10, 10)
diag(mat) <- 0
cqual(mat, c(1,1,1,2,2,2,3,3,3,3))
#> Cluster Quality Metrics
#> =======================
#> 
#> Global metrics:
#>   Modularity: -0.1139 
#>   Coverage:   0.2214 
#>   Clusters:   3 
#> 
#> Per-cluster metrics:
#>  cluster cluster_name n_nodes internal_edges cut_edges internal_density
#>        1            1       3       2.609745  23.94103        0.4349575
#>        2            2       3       3.044833  24.35574        0.5074722
#>        3            3       4       5.093286  27.31874        0.4244405
#>  avg_internal_degree expansion cut_ratio conductance
#>             1.739830  7.980343  1.140049   0.8210083
#>             2.029889  8.118581  1.159797   0.7999808
#>             2.546643  6.829684  1.138281   0.7283965