Package index • grip

Layout computation

Compute graph layouts using the multiscale GRIP algorithm.

grip(): Compute a GRIP layout
globalrep.grip(): Compute a GRIP layout with coarse global repulsion
legacy.grip(): Compute the legacy GRIP layout
trace.grip(): Compute a GRIP layout trace
trace.legacy.grip(): Compute a trace for the legacy GRIP layout

Quality metrics

Score and compare layouts across seeds and parameter settings.

score.layout(): Score a single layout using graph-aware quality heuristics
geometry.diagnostics(): Geometry-aware diagnostics against a canonical target
compare.layouts(): Compare multiple layout candidates across seeds
params.from.summary(): Extract layout parameters from a comparison summary row

Landmark geodesic KK

Prepare, score, and optimize layouts with the sparse landmark-geodesic KK objective.

prepare.landmark.geodesic.kk(): Prepare sparse landmark-geodesic KK data for repeated layout evaluation
score.landmark.geodesic.kk(): Score a layout under the landmark geodesic KK energy
landmark.geodesic.kk(): Optimize a layout under the landmark geodesic KK energy

Weighted layout computation

Compute geometry-aware layouts and multiscale filtrations for weighted graphs.

weighted.grip(): Alias of globalrep.weighted.grip()
weighted.grip.nd(): Weighted GRIP layout in arbitrary dimensions
globalrep.weighted.grip(): Compute a weighted geometry-aware GRIP layout
trace.weighted.grip(): Trace a weighted geometry-aware GRIP layout
build.misf(): Build a maximal independent set filtration (MISF) for a graph
build.weighted.misf(): Build a weighted MISF hierarchy

Geodesic MDS and edge optimization

Score, initialize, and polish weighted layouts with GMDS-oriented objectives.

score.gmds(): Score a layout with the common GMDS diagnostic panel
gmds.result(): Construct a common GMDS layout result
metric.mds(): Metric-MDS baseline layout for GMDS experiments
prepare.graph.geodesic.mds(): Prepare a graph-first geodesic-MDS path cache
edge.length.density.stiffness(): Construct edge-length stiffnesses for edge-isometric GMDS layouts
prepare.edge.kk(): Prepare an edge-only graph for edge-KK repair
grip.prepare.edge.kk(): Deprecated edge-KK preparation name
edge.kk(): Optimize an edge-KK local repair layout
grip.optimize.edge.kk.layout() grip.optimize.edge.gkk.layout() grip.optimize.edge.isometric.layout(): Deprecated edge-KK layout names
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

Full geodesic KK

Prepare, score, and optimize layouts under the full geodesic Kamada-Kawai objective.

prepare.geodesic.kk(): Prepare full geodesic KK data for repeated layout evaluation
score.geodesic.kk(): Score a layout under the full geodesic KK energy
geodesic.kk(): Optimize a layout under the full geodesic KK energy

MISF Geodesic KK

Prepare, score, and optimize multiscale geodesic-KK layouts using MISF hierarchies.

prepare.misf.geodesic.kk(): Prepare a MISF-based multiscale geodesic-KK object
score.misf.geodesic.kk(): Score a MISF-based geodesic-KK fit
misf.geodesic.kk(): Optimize an embedding with the MISF-based geodesic-KK pipeline

Visualization

Plot layouts in 2D and 3D.

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

Graph generators

Build common graph families as edge-list matrices.

edges.path() edges.cycle() edges.mesh() edges.occupied.mesh() edges.cylinder() edges.torus() edges.irregular.ball() edges.irregular.shell() edges.irregular.torus() edges.sphere() edges.irregular.annulus() edges.irregular.pair.of.pants() edges.irregular.double.torus() edges.irregular.sphere() edges.cube() edges.kary.tree() edges.recursive.mask.grid() edges.recursive.triangle.mask() edges.recursive.tetrahedron.mask() edges.recursive.cube.mask() edges.triangulated.polyhedron() edges.triangulated.annulus() edges.triangulated.pair.of.pants() edges.vicsek() edges.menger.sponge() edges.cube.periodic.tunnels() edges.cube.asymmetric.cavities() edges.cube.channel.network() edges.sierpinski.triangle() edges.sierpinski.tetrahedron() edges.sierpinski.carpet(): Sample graph generators

Surface family helpers

Helper topics for weighted surface, solid, occupied-mesh, and tree graph families.

mesh.surface.embedding() mesh.surface.graph(): Weighted mesh surface helpers
sampled.rectangle.param.coords() sampled.rectangle.surface.embedding() sampled.rectangle.surface.graph() sampled.rectangle.surface.graphs(): Sampled rectangle surface helpers
cylinder.surface.embedding() cylinder.surface.graph(): Weighted cylinder surface helpers
sphere.surface.embedding() sphere.surface.graph(): Weighted sphere surface helpers
torus.surface.embedding() torus.surface.graph(): Weighted torus surface helpers
irregular.rectangle.param.coords() irregular.rectangle.surface.embedding() irregular.rectangle.surface.graph(): Irregular rectangle surface helpers
irregular.annulus.surface.embedding() irregular.annulus.surface.graph(): Weighted irregular annulus surface helpers
irregular.sphere.surface.embedding() irregular.sphere.surface.graph(): Weighted irregular sphere surface helpers
irregular.torus.surface.embedding() irregular.torus.surface.graph(): Weighted irregular torus surface helpers
irregular.double.torus.surface.embedding() irregular.double.torus.surface.graph(): Weighted irregular double-torus surface helpers
irregular.pair.of.pants.surface.embedding() irregular.pair.of.pants.surface.graph(): Weighted irregular pair-of-pants surface helpers
irregular.ball.solid.embedding() irregular.ball.solid.graph(): Weighted irregular ball solid helpers
irregular.shell.solid.embedding() irregular.shell.solid.graph(): Weighted irregular shell solid helpers
triangulated.annulus.surface.embedding() triangulated.annulus.surface.graph(): Weighted triangulated annulus surface helpers
triangulated.pair.of.pants.surface.embedding() triangulated.pair.of.pants.surface.graph(): Weighted triangulated pair-of-pants surface helpers
triangulated.polyhedron.surface.embedding() triangulated.polyhedron.surface.graph(): Weighted triangulated polyhedron surface helpers
occupied.mesh.surface.embedding() occupied.mesh.surface.graph(): Occupied-mesh and perforated-grid helpers
keep.periodic.holes() keep.staggered.windows() keep.slit.channels() keep.asymmetric.notches(): Deterministic perforated-grid occupancy helpers
kary.tree.weighted.graph(): Intrinsically weighted k-ary tree helpers

Recursive and fractal family helpers

Helper topics for recursive masks, porous families, and self-similar graph generators.

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

Interactive explorer

Shiny-based layout browser for interactive exploration.

gripui_app(): Build the `gripui` Shiny application
run_gripui(): Run the `gripui` Shiny application
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_family_app(): Build the graph-family geometry explorer Shiny application
run_gripui_family(): Run the graph-family geometry explorer Shiny application
gripui_graph_family_catalog(): Catalog of graph families for the geometry explorer app

Data

Bundled datasets for examples and vignettes.

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

Package

grip-package: grip: Graph dRawing with Intelligent Placement
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.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.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(): Deprecated long-form API names
grip.score.layout(): Deprecated layout scoring name
grip.compare.layouts(): Deprecated layout comparison name