piglet (version 1.2.0)

optimize_resolution: Optimize resolution parameter using silhouette score

Description

Performs a grid search over resolution parameters and selects the one that maximizes the silhouette score.

Usage

optimize_resolution(
  g,
  distance_matrix,
  target_clusters = 80,
  resolution_range_low = 0.1,
  resolution_range_high = 0.5,
  max_steps = 20,
  ncores = 1
)

Value

A list containing:

• results: data.frame with Resolution, ClusterCount, Silhouette

• partitions: list of membership vectors for each resolution

• best_resolution: optimal resolution parameter

• best_partition: membership vector at optimal resolution

• best_clusters: number of clusters at optimal resolution

Arguments

g

An igraph graph object with weighted edges

distance_matrix

The distance matrix (as dist object) used for silhouette calculation

target_clusters

Target number of clusters for initial tuning. Default is 80.

resolution_range_low

Fractional range below tuned resolution. Default is 0.1.

resolution_range_high

Fractional range above tuned resolution. Default is 0.5.

max_steps

Maximum steps for initial tuning. Default is 20.

ncores

Number of cores for parallel processing. Default is 1.

See Also

detect_communities_leiden, igClust