# Graph Drawing with Intelligent Placement (GRIP)

## Documentation for package ‘grip’ version 0.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

B C E G H I K L M O P R S T V W

grip-package | grip: Graph dRawing with Intelligent Placement

## -- B --

build.misf | Build a maximal independent set filtration (MISF) for a graph
build.weighted.misf | Build a weighted MISF hierarchy

## -- C --

compare.layouts | Compare multiple layout candidates across seeds
cube.asymmetric.cavities.surface.graph | Weighted porous cube-mask surface helpers
cube.channel.network.surface.graph | Weighted porous cube-mask surface helpers
cube.periodic.tunnels.surface.graph | Weighted porous cube-mask surface helpers
cube_mask_pattern_helpers | Cube mask pattern helpers for recursive porous families
cylinder.surface.graph | Weighted cylinder surface helpers
cylinder_surface_helpers | Weighted cylinder surface helpers

## -- E --

edge.kk | Optimize an edge-KK local repair layout
edge.length.density.stiffness | Construct edge-length stiffnesses for edge-isometric GMDS layouts
edge.repulsive.stage | Optimize one edge-isometric repulsive unfolding stage
edge.repulsive.state | Evaluate an edge-isometric repulsive unfolding objective
edges.cube | Sample graph generators
edges.cycle | Sample graph generators
edges.cylinder | Sample graph generators
edges.kary.tree | Sample graph generators
edges.mesh | Sample graph generators
edges.path | Sample graph generators
edges.sierpinski.carpet | Sample graph generators
edges.sierpinski.tetrahedron | Sample graph generators
edges.sierpinski.triangle | Sample graph generators
edges.torus | Sample graph generators

## -- G --

geodesic.kk | Optimize a layout under the full geodesic KK energy
geometry.diagnostics | Geometry-aware diagnostics against a canonical target
globalrep.grip | Compute a GRIP layout with coarse global repulsion
globalrep.weighted.grip | Compute a weighted geometry-aware GRIP layout
graph.riemannian.star.structure | Build a local Riemannian star structure for Gram-gKK layouts
graph_generators | Sample graph generators
grip | Compute a GRIP layout
grip-0.2-migration | Migrate code to the grip 0.2 API
grip.build.misf | Migrate code to the grip 0.2 API
grip.build.misf.weighted | Migrate code to the grip 0.2 API
grip.compare.layouts | Migrate code to the grip 0.2 API
grip.edge.length.density.stiffness | Migrate code to the grip 0.2 API
grip.edge.repulsive.state | Migrate code to the grip 0.2 API
grip.geometry.diagnostics | Migrate code to the grip 0.2 API
grip.gmds.layout.result | Migrate code to the grip 0.2 API
grip.layout | Migrate code to the grip 0.2 API
grip.layout.globalrep | Migrate code to the grip 0.2 API
grip.layout.globalrep.weighted | Migrate code to the grip 0.2 API
grip.layout.legacy | Migrate code to the grip 0.2 API
grip.layout.trace | Migrate code to the grip 0.2 API
grip.layout.trace.legacy | Migrate code to the grip 0.2 API
grip.layout.trace.weighted | Migrate code to the grip 0.2 API
grip.layout.weighted | Migrate code to the grip 0.2 API
grip.layout.weighted.nd | Migrate code to the grip 0.2 API
grip.metric.mds.layout | Migrate code to the grip 0.2 API
grip.optimize.edge.gkk.layout | Migrate code to the grip 0.2 API
grip.optimize.edge.isometric.layout | Migrate code to the grip 0.2 API
grip.optimize.edge.kk.layout | Migrate code to the grip 0.2 API
grip.optimize.edge.repulsive.stage | Migrate code to the grip 0.2 API
grip.optimize.geodesic.kk | Migrate code to the grip 0.2 API
grip.optimize.kernel.gram.gkk.layout | Migrate code to the grip 0.2 API
grip.optimize.landmark.geodesic.kk | Migrate code to the grip 0.2 API
grip.optimize.misf.geodesic.kk | Migrate code to the grip 0.2 API
grip.optimize.repulsive.stage | Migrate code to the grip 0.2 API
grip.params.from.summary | Migrate code to the grip 0.2 API
grip.plot | Migrate code to the grip 0.2 API
grip.prepare.edge.kk | Migrate code to the grip 0.2 API
grip.prepare.geodesic.kk | Migrate code to the grip 0.2 API
grip.prepare.graph.geodesic.mds | Migrate code to the grip 0.2 API
grip.prepare.landmark.geodesic.kk | Migrate code to the grip 0.2 API
grip.prepare.misf.geodesic.kk | Migrate code to the grip 0.2 API
grip.project.3d | Migrate code to the grip 0.2 API
grip.repulsive.state | Migrate code to the grip 0.2 API
grip.score.geodesic.kk | Migrate code to the grip 0.2 API
grip.score.gmds.layout | Migrate code to the grip 0.2 API
grip.score.landmark.geodesic.kk | Migrate code to the grip 0.2 API
grip.score.layout | Migrate code to the grip 0.2 API
grip.score.misf.geodesic.kk | Migrate code to the grip 0.2 API
gripui_app | Build the 'gripui' Shiny application
gripui_family_app | Build the graph-family geometry explorer Shiny application
gripui_graph_family_catalog | Catalog of graph families for the geometry explorer app
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'

## -- H --

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

## -- I --

irregular.annulus.surface.graph | Weighted irregular annulus surface helpers
irregular.ball.solid.graph | Weighted irregular ball solid 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.rectangle.surface.graph | Irregular rectangle surface helpers
irregular.shell.solid.graph | Weighted irregular shell solid helpers
irregular.sphere.surface.graph | Weighted irregular sphere surface helpers
irregular.torus.surface.graph | Weighted irregular torus surface helpers
irregular_annulus_surface_helpers | Weighted irregular annulus surface helpers
irregular_ball_solid_helpers | Weighted irregular ball solid helpers
irregular_double_torus_surface_helpers | Weighted irregular double-torus surface helpers
irregular_pair_of_pants_surface_helpers | Weighted irregular pair-of-pants surface helpers
irregular_rectangle_surface_helpers | Irregular rectangle surface helpers
irregular_shell_solid_helpers | Weighted irregular shell solid helpers
irregular_sphere_surface_helpers | Weighted irregular sphere surface helpers
irregular_torus_surface_helpers | Weighted irregular torus surface helpers

## -- K --

kary.tree.weighted.graph | Intrinsically weighted k-ary tree helpers
kary_tree_weighted_graph_helpers | Intrinsically weighted k-ary tree helpers
keep.asymmetric.notches | Deterministic perforated-grid occupancy helpers
keep.periodic.holes | Deterministic perforated-grid occupancy helpers
keep.slit.channels | Deterministic perforated-grid occupancy helpers
keep.staggered.windows | Deterministic perforated-grid occupancy helpers
kernel.gram.gkk | Optimize a kernel Gram-gKK layout

## -- L --

landmark.geodesic.kk | Optimize a layout under the landmark geodesic KK energy
legacy.grip | Compute the legacy GRIP layout

## -- M --

mask.asymmetric.holes | Mask pattern helpers for recursive grid families
mask.border | Mask pattern helpers for recursive grid families
mask.corner | Mask pattern helpers for recursive grid families
mask.cross | Mask pattern helpers for recursive grid families
mask.cube.asymmetric.cavities | Cube mask pattern helpers for recursive porous families
mask.cube.channel.network | Cube mask pattern helpers for recursive porous families
mask.cube.periodic.tunnels | Cube mask pattern helpers for recursive porous families
mask.tetrahedron.classic | Tetrahedron mask helpers for recursive gasket families
mask.tetrahedron.corner.missing | Tetrahedron mask helpers for recursive gasket families
mask.triangle.bridge | Triangle mask helpers for recursive gasket families
mask.triangle.classic | Triangle mask helpers for recursive gasket families
mask_pattern_helpers | Mask pattern helpers for recursive grid families
menger.sponge.surface.graph | Weighted Menger sponge surface helpers
menger_sponge_surface_helpers | Weighted Menger sponge surface helpers
mesh.surface.graph | Weighted mesh surface helpers
mesh_surface_helpers | Weighted mesh surface helpers
metric.mds | Metric-MDS baseline layout for GMDS experiments
misf.geodesic.kk | Optimize an embedding with the MISF-based geodesic-KK pipeline

## -- O --

occupied.mesh.surface.graph | Occupied-mesh and perforated-grid helpers
occupied_mesh_surface_helpers | Occupied-mesh and perforated-grid helpers

## -- P --

params.from.summary | Extract layout parameters from a comparison summary row
perforated_grid_helpers | Deterministic perforated-grid occupancy helpers
plot.layout | Quick plot for graph layouts
porous_cube_surface_helpers | Weighted porous cube-mask surface helpers
prepare.edge.kk | Prepare an edge-only graph for edge-KK repair
prepare.geodesic.kk | Prepare full geodesic KK data for repeated layout evaluation
prepare.graph.geodesic.mds | Prepare a graph-first geodesic-MDS path cache
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
project.3d | Project 3D coordinates to 2D for static plotting

## -- R --

recursive.cube.mask.surface.graph | Weighted recursive cube-mask surface helpers
recursive.mask.grid.surface.graph | Weighted recursive mask-grid surface helpers
recursive.tetrahedron.mask.surface.graph | Weighted recursive tetrahedron-mask surface helpers
recursive.triangle.mask.surface.graph | Weighted recursive triangle-mask surface helpers
recursive_cube_mask_surface_helpers | Weighted recursive cube-mask surface helpers
recursive_mask_grid_surface_helpers | Weighted recursive mask-grid surface helpers
recursive_tetrahedron_mask_surface_helpers | Weighted recursive tetrahedron-mask surface helpers
recursive_triangle_mask_surface_helpers | Weighted recursive triangle-mask surface helpers
repulsive.stage | Optimize one pure repulsive layout stage
repulsive.state | Evaluate a pure repulsive layout objective
run_gripui | Run the 'gripui' Shiny application
run_gripui_family | Run the graph-family geometry explorer Shiny application

## -- S --

sampled.rectangle.surface.graph | Sampled rectangle surface helpers
sampled.rectangle.surface.graphs | Sampled rectangle surface helpers
sampled_rectangle_surface_helpers | Sampled rectangle surface helpers
score.geodesic.kk | Score a layout under the full geodesic KK energy
score.gmds | Score a layout with the common GMDS diagnostic panel
score.landmark.geodesic.kk | Score a layout under the landmark geodesic KK energy
score.layout | Score a single layout using graph-aware quality heuristics
score.misf.geodesic.kk | Score a MISF-based geodesic-KK fit
sierpinski.carpet.surface.graph | Weighted Sierpinski carpet surface helpers
sierpinski.tetrahedron.surface.graph | Weighted Sierpinski tetrahedron surface helpers
sierpinski.triangle.surface.graph | Weighted Sierpinski triangle surface helpers
sierpinski_carpet_surface_helpers | Weighted Sierpinski carpet surface helpers
sierpinski_tetrahedron_surface_helpers | Weighted Sierpinski tetrahedron surface helpers
sierpinski_triangle_surface_helpers | Weighted Sierpinski triangle surface helpers
sphere.surface.graph | Weighted sphere surface helpers
sphere_surface_helpers | Weighted sphere surface helpers

## -- T --

tetrahedron_mask_helpers | Tetrahedron mask helpers for recursive gasket families
torus.surface.graph | Weighted torus surface helpers
torus_surface_helpers | Weighted torus surface helpers
trace.grip | Trace a GRIP layout
trace.legacy.grip | Compute a trace for the legacy GRIP layout
triangle_mask_helpers | Triangle mask helpers for recursive gasket families
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
triangulated_annulus_surface_helpers | Weighted triangulated annulus surface helpers
triangulated_pair_of_pants_surface_helpers | Weighted triangulated pair-of-pants surface helpers
triangulated_polyhedron_surface_helpers | Weighted triangulated polyhedron surface helpers

## -- V --

vicsek.surface.graph | Weighted Vicsek surface helpers
vicsek_surface_helpers | Weighted Vicsek surface helpers

## -- W --

weighted.grip.nd | Weighted GRIP layout in arbitrary dimensions