Score a layout with the common GMDS diagnostic panel
Source:R/gmds_layout_interface.R
score.gmds.Rd`score.gmds()` provides a common diagnostic panel for GMDS-oriented layouts. It summarizes edge-length fidelity, fixed-path geodesic stress, short/mid/long geodesic bands, ordinary metric-MDS chord stress, and simple spread/shortcut diagnostics for any coordinate matrix on a prepared graph.
Usage
score.gmds(
coords,
prepared = NULL,
edges = NULL,
n = NULL,
adj_list = NULL,
weight_list = NULL,
edge_weights = NULL,
scale_mode = c("profiled", "identity", "user"),
edge_scale = NULL,
path_scale = NULL,
chord_scale = NULL,
distance_floor = 1e-08,
edge_length_epsilon = 1e-08,
band_quantiles = c(1/3, 2/3)
)Arguments
- coords
Numeric coordinate matrix.
- prepared
Optional object returned by [prepare.edge.kk()], [prepare.graph.geodesic.mds()] or [prepare.geodesic.kk()]. Edge-only objects from [prepare.edge.kk()] report only edge diagnostics; all-pairs GMDS path and chord diagnostics are unavailable.
- edges
Two-column edge matrix used when `prepared` is omitted.
- n
Number of vertices used when `prepared` is omitted.
- adj_list
Optional adjacency list used when `prepared` is omitted.
- weight_list
Optional edge-weight list parallel to `adj_list`.
- edge_weights
Optional positive edge weights parallel to `edges`.
- scale_mode
Scale policy for edge, path, and chord targets: `"profiled"` fits one scalar for each diagnostic family, `"identity"` uses scale one, and `"user"` uses the corresponding supplied scale.
- edge_scale, path_scale, chord_scale
Optional user scales used when `scale_mode = "user"`.
- distance_floor
Positive floor for relative residuals.
- edge_length_epsilon
Small stabilizer for fixed-path embedded lengths.
- band_quantiles
Two quantiles splitting graph distances into short, mid, and long bands.