Graph Drawing with Intelligent Placement (GRIP)
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Documentation for package ‘grip’ version 0.2.0
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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 |