Package index

Compute layouts

grip(): Compute a GRIP layout
weighted.grip.nd(): Weighted GRIP layout in arbitrary dimensions
classical.mds(): Classical-MDS baseline layout for GMDS experiments
metric.mds(): Metric stress MDS using SMACOF
globalrep.grip(): Compute a GRIP layout with coarse global repulsion
globalrep.weighted.grip(): Compute a weighted geometry-aware GRIP layout
legacy.grip(): Compute the legacy GRIP layout

Select and compare candidates

compare.layouts(): Compare multiple layout candidates across seeds
params.from.summary(): Extract layout parameters from a comparison summary row

Score graph distances or reference geometry

score.layout(): Score a single layout using graph-aware quality heuristics
score.gmds(): Score a layout with the common GMDS diagnostic panel
score.coordinates(): Score coordinates against corresponding reference observations
score.surface(): Estimate symmetric area-weighted distance between triangular surfaces
geometry.diagnostics(): Geometry-aware diagnostics against a canonical target

Trace multiscale layouts

trace.grip(): Trace a GRIP layout
trace.legacy.grip(): Compute a trace for the legacy GRIP layout

Plot and project

layout.coords(): Extract coordinates from a layout result
plot(<layout>): Quick plot for graph layouts
project.3d(): Project 3D coordinates to 2D for static plotting

Prepare graphs and inspect multiscale structures

build.misf(): Build a maximal independent set filtration (MISF) for a graph
build.weighted.misf(): Build a weighted MISF hierarchy
estimate.preparation(): Estimate preparation storage before allocating graph distances
prepare.edge.kk(): Prepare an edge-only graph for edge-KK repair
prepare.graph.geodesic.mds(): Prepare a graph-first geodesic-MDS path cache
prepare.geodesic.kk(): Prepare full geodesic KK data for repeated layout evaluation
prepare.landmark.geodesic.kk(): Prepare sparse landmark-geodesic KK data for repeated layout evaluation
prepare.misf.geodesic.kk(): Prepare a MISF-based multiscale geodesic-KK object

edge.kk(): Optimize an edge-KK local repair layout
edge.length.density.stiffness(): Construct edge-length stiffnesses for edge-isometric GMDS layouts
geodesic.kk(): Optimize a layout under the full geodesic KK energy
score.geodesic.kk(): Score a layout under the full geodesic KK energy
landmark.geodesic.kk(): Optimize a layout under the landmark geodesic KK energy
score.landmark.geodesic.kk(): Score a layout under the landmark geodesic KK energy
misf.geodesic.kk(): Optimize an embedding with the MISF-based geodesic-KK pipeline
score.misf.geodesic.kk(): Score a MISF-based geodesic-KK fit
edge.repulsive.state(): Evaluate an edge-isometric repulsive unfolding objective
edge.repulsive.stage(): Optimize one edge-isometric repulsive unfolding stage
repulsive.state(): Evaluate a pure repulsive layout objective
repulsive.stage(): Optimize one pure repulsive layout stage
graph.riemannian.star.structure(): Build a local Riemannian star structure for Gram-gKK layouts
kernel.gram.gkk(): Optimize a kernel Gram-gKK layout

Synthetic graphs: primitive edge generators

edges.path() edges.cycle() edges.mesh() edges.cylinder() edges.torus() edges.cube() edges.kary.tree() edges.sierpinski.triangle() edges.sierpinski.tetrahedron() edges.sierpinski.carpet(): Sample graph generators

Synthetic graphs: configurable keep masks

keep.periodic.holes() keep.staggered.windows() keep.slit.channels() keep.asymmetric.notches(): Deterministic perforated-grid occupancy helpers
mask.cross() mask.border() mask.corner() mask.asymmetric.holes(): Mask pattern helpers for recursive grid families
mask.cube.periodic.tunnels() mask.cube.asymmetric.cavities() mask.cube.channel.network(): Cube mask pattern helpers for recursive porous families
mask.triangle.classic() mask.triangle.bridge(): Triangle mask helpers for recursive gasket families
mask.tetrahedron.classic() mask.tetrahedron.corner.missing(): Tetrahedron mask helpers for recursive gasket families

Synthetic graphs: complete surface and solid bundles

mesh.surface.graph(): Weighted mesh surface helpers
occupied.mesh.surface.graph(): Occupied-mesh and perforated-grid helpers
cylinder.surface.graph(): Weighted cylinder surface helpers
sphere.surface.graph(): Weighted sphere surface helpers
torus.surface.graph(): Weighted torus surface helpers
irregular.rectangle.surface.graph(): Irregular rectangle surface helpers
irregular.annulus.surface.graph(): Weighted irregular annulus surface helpers
irregular.sphere.surface.graph(): Weighted irregular sphere surface helpers
irregular.torus.surface.graph(): Weighted irregular torus surface helpers
irregular.double.torus.surface.graph(): Weighted irregular double-torus surface helpers
irregular.pair.of.pants.surface.graph(): Weighted irregular pair-of-pants surface helpers
irregular.ball.solid.graph(): Weighted irregular ball solid helpers
irregular.shell.solid.graph(): Weighted irregular shell solid helpers
triangulated.annulus.surface.graph(): Weighted triangulated annulus surface helpers
triangulated.pair.of.pants.surface.graph(): Weighted triangulated pair-of-pants surface helpers
triangulated.polyhedron.surface.graph(): Weighted triangulated polyhedron surface helpers
sampled.rectangle.surface.graph() sampled.rectangle.surface.graphs(): Sampled rectangle surface helpers
kary.tree.weighted.graph(): Intrinsically weighted k-ary tree helpers

Synthetic graphs: complete recursive bundles

recursive.mask.grid.surface.graph(): Weighted recursive mask-grid surface helpers
recursive.cube.mask.surface.graph(): Weighted recursive cube-mask surface helpers
recursive.triangle.mask.surface.graph(): Weighted recursive triangle-mask surface helpers
recursive.tetrahedron.mask.surface.graph(): Weighted recursive tetrahedron-mask surface helpers
sierpinski.carpet.surface.graph(): Weighted Sierpinski carpet surface helpers
sierpinski.triangle.surface.graph(): Weighted Sierpinski triangle surface helpers
sierpinski.tetrahedron.surface.graph(): Weighted Sierpinski tetrahedron surface helpers
menger.sponge.surface.graph(): Weighted Menger sponge surface helpers
vicsek.surface.graph(): Weighted Vicsek surface helpers
cube.periodic.tunnels.surface.graph() cube.asymmetric.cavities.surface.graph() cube.channel.network.surface.graph(): Weighted porous cube-mask surface helpers

Interactive exploration

gripui_project(): Create a normalized gripui project object
gripui_project_from_compare(): Convert compare.layouts() output into a gripui_project
gripui_project_from_dir(): Create a gripui_project from a directory of saved artifacts
gripui_validate_project(): Validate a gripui_project
gripui_app(): Build the gripui Shiny application
run_gripui(): Run the gripui Shiny application
gripui_graph_family_catalog(): Catalog of graph families for the geometry explorer app
gripui_family_app(): Build the graph-family geometry explorer Shiny application
run_gripui_family(): Run the graph-family geometry explorer Shiny application

Object methods

print(<grip_gmds_layout>): Print a geodesic-MDS layout summary
print(<grip_misf>): Print a multiscale hierarchy summary

Data

hmp.gc: HMP Illumina 16S Giant-Component Graph
hmp.u01.gc.coarse: HMP/U01 Coarsened Giant-Component Graph

Package and migration

grip-package: grip: Graph dRawing with Intelligent Placement
grip-0.2-migration grip.layout grip.layout.globalrep grip.layout.globalrep.weighted grip.layout.legacy grip.layout.trace grip.layout.trace.legacy grip.layout.trace.weighted grip.layout.weighted grip.layout.weighted.nd grip.plot grip.project.3d grip.metric.mds.layout grip.optimize.kernel.gram.gkk.layout grip.score.gmds.layout grip.gmds.layout.result grip.edge.length.density.stiffness grip.prepare.landmark.geodesic.kk grip.prepare.geodesic.kk grip.prepare.graph.geodesic.mds grip.prepare.misf.geodesic.kk grip.prepare.edge.kk grip.score.landmark.geodesic.kk grip.score.geodesic.kk grip.score.misf.geodesic.kk grip.optimize.landmark.geodesic.kk grip.optimize.geodesic.kk grip.optimize.misf.geodesic.kk grip.optimize.edge.kk.layout grip.optimize.edge.gkk.layout grip.optimize.edge.isometric.layout grip.optimize.edge.repulsive.stage grip.optimize.repulsive.stage grip.edge.repulsive.state grip.repulsive.state grip.build.misf.weighted grip.build.misf grip.geometry.diagnostics grip.params.from.summary grip.score.layout grip.compare.layouts: Migrate code to the grip 0.2 API
grip-mds-migration: Migrating classical and metric stress MDS workflows

Compute layouts

Select and compare candidates

Score graph distances or reference geometry

Trace multiscale layouts

Plot and project

Prepare graphs and inspect multiscale structures

Experimental refinement and state diagnostics

Synthetic graphs: primitive edge generators

Synthetic graphs: configurable keep masks

Synthetic graphs: complete surface and solid bundles

Synthetic graphs: complete recursive bundles

Interactive exploration

Object methods

Data

Package and migration