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Metric-MDS baseline layout for GMDS experiments

Source: R/gmds_layout_interface.R
metric.mds.Rd

`metric.mds()` computes the current metric-MDS baseline using `stats::cmdscale()` on the graph shortest-path distance matrix and returns a common `"grip_gmds_layout"` result.

Usage

metric.mds(
  prepared = NULL,
  edges = NULL,
  n = NULL,
  adj_list = NULL,
  weight_list = NULL,
  edge_weights = NULL,
  dim = 2L,
  add = FALSE,
  eig = TRUE,
  diagnostics = TRUE,
  scale_mode = c("profiled", "identity", "user"),
  distance_floor = 1e-08,
  edge_length_epsilon = 1e-08,
  band_quantiles = c(1/3, 2/3)
)

Arguments

prepared

Optional all-pairs prepared object returned by [prepare.graph.geodesic.mds()] or [prepare.geodesic.kk()]. Edge-only objects from [prepare.edge.kk()] are intentionally rejected because metric MDS requires a graph distance matrix.

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`.

dim

Target embedding dimension. Values greater than 3 are supported for GMDS and edge-KK workflows.

add, eig

Passed to `stats::cmdscale()`.

diagnostics

If `TRUE`, attach the common GMDS diagnostic panel. If `FALSE` and raw graph inputs are supplied, `metric.mds()` uses a distance-matrix-only preparation path and does not build the full all-pairs path cache.

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.

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.

Value

A `"grip_gmds_layout"` object.