Score a layout under the full geodesic KK energy

score.geodesic.kk() evaluates a layout using the full all-pairs geodesic Kamada–Kawai objective. Distances are measured along fixed chosen graph shortest paths, not by straight-line chord length.

Usage

score.geodesic.kk(
  coords,
  prepared = NULL,
  edges = NULL,
  n = NULL,
  adj_list = NULL,
  weight_list = NULL,
  edge_weights = NULL,
  stiffness = 1,
  distance_floor = 1e-08,
  edge_length_epsilon = 1e-08,
  scale_mode = c("profiled", "user"),
  scale.L0 = NULL,
  return_pair_details = FALSE
)

Arguments

coords: Numeric coordinate matrix with 2 or 3 columns.
prepared: Optional object returned by prepare.geodesic.kk().
edges: Two-column integer matrix of edges (1-based vertex ids).
n: Number of vertices.
adj_list: Adjacency list (1-based) for an undirected graph.
weight_list: Optional parallel list of positive edge weights.
edge_weights: Optional positive edge-weight vector parallel to edges.
stiffness: Global stiffness constant \(K\).
distance_floor: Small positive floor used in k_ij = K / max(g_ij, distance_floor)^2.
edge_length_epsilon: Small positive stabilizer added inside each embedded edge length.
scale_mode: Either "profiled" to fit L0 analytically for the supplied layout or "user" to use scale.L0.
scale.L0: Optional user-supplied geodesic KK scale, required when scale_mode = "user".
return_pair_details: If TRUE, include pairwise path lengths and residuals in a list column.

Value

A one-row data frame with the fitted or user-supplied scale factor and full geodesic KK energy summary.

Details

By default the global target scale L0 is fit analytically for the supplied layout. Alternatively, the score can be evaluated at a user-supplied scale.