Data-Derived Graph Construction Utilities
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Documentation for package ‘dgraphs’ version 0.1.0
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A B C D E G I J L M N O P R S V W
-- A --
| adjlist.to.igraph | Convert an Adjacency List to igraph |
| as_igraph | Convert a Basin Graph to igraph |
-- B --
| build.iknn.graphs.and.selectk | Build iKNN Graphs and Select a Neighborhood Size |
-- C --
| calculate.edit.distances | Calculate Edit Distances Between Sequential Graphs |
| compare.adj.lists | Compare Two Adjacency Lists |
| compare.paths | Compare Paths Across Hop Limits |
| compute.geodesic.stats | Compute Geodesic Statistics for Grid Vertices |
| compute.graph.diameter | Compute a Weighted Graph Diameter |
| compute.graph.distance | Compute a Weighted Shortest-Path Distance |
| compute.graph.endpoint.scores | Compute Graph Endpoint Scores from a 3D Embedding |
| compute.graph.summary.pmf | Compute a graph summary as a probability mass function |
| compute.graph.summary.stability | Compute graph-summary stability across a graph sequence |
| compute.stability.metrics | Compute Stability Metrics Across a Sequence of IkNN Graphs |
| compute.vertex.geodesic.stats | Compute Geodesic Statistics for a Single Grid Vertex |
| convert.adjacency.list.to.adjacency.matrix | Convert an Adjacency List to an Adjacency Matrix |
| convert.adjacency.to.edge.matrix | Convert an Adjacency List to an Edge Matrix |
| convert.to.undirected | Convert a Directed Adjacency List to an Undirected Adjacency List |
| convert.weighted.adjacency.matrix.to.adjacency.list | Convert a Weighted Adjacency Matrix to Lists |
| count.edges | Count Edges in an Undirected Adjacency List |
| cpp.create.rknn.graphs | Compute Adaptive Radius-kNN Graphs With Batched ANN Search |
| create.adaptive.radius.graph | Deprecated Radius Graph Constructors |
| create.bi.kNN.chain.graph | Create a Bi-kNN Chain Graph |
| create.bipartite.graph | Create a Bipartite Graph |
| create.chain.graph | Create a Chain Graph |
| create.chain.graph.with.offset | Create a Chain Graph with Offset Vertex Labels |
| create.circular.graph | Create a Circular Graph |
| create.cknn.graph | Compute a Continuous-kNN Graph |
| create.cmst.graph | Construct a Minimal Spanning Tree (MST) Completion Graph |
| create.complete.graph | Create a Complete Graph |
| create.distance.plot | Create Distance Plot |
| create.empty.graph | Create an Empty Graph |
| create.geodesic.iknn.graph | Create a graph-geodesic iKNN graph |
| create.grid.graph | Create a Refined Graph with Approximately Uniform Edge Spacing |
| create.iknn.graphs | Create intersection k-nearest neighbor graphs with dual pruning |
| create.iterated.iknn.graphs | Create iterated graph-geodesic iKNN graphs |
| create.maximal.packing | Create a Maximal Packing of Vertices in a Graph |
| create.mknn.graph | Compute a Mutual k-Nearest Neighbor Graph with Weights |
| create.mknn.graphs | Create Multiple Mutual kNN Graphs with Geometric Pruning |
| create.path.graph | Create a Path Graph with Limited Hop Distance |
| create.path.graph.series | Create a Series of Path Graphs |
| create.plm.graph | Create a Path Length Matrix Graph Structure |
| create.radius.graph | Deprecated Radius Graph Constructors |
| create.random.graph | Create a Random Undirected Graph |
| create.rknn.graph | Compute a Radius-kNN Graph |
| create.rknn.graphs | Compute Adaptive Radius-kNN Graphs Across k Values |
| create.single.iknn.graph | Create a Single Intersection-weighted k-Nearest Neighbors Graph |
| create.sknn.graph | Compute a Symmetric k-Nearest Neighbor Graph |
| create.star.graph | Create a Star Graph by Joining Chains |
| create.subgraph | Create a Subgraph from a Graph Object |
| create.threshold.distance.graph | Create a Threshold Distance Graph |
-- D --
| deprecated-radius-graph-constructors | Deprecated Radius Graph Constructors |
| detect.graph.endpoints | Detect Graph Endpoints from a 3D Embedding |
| detect.local.extrema | Detect Local Extrema in a Graph |
| dist.to.knn | Produce k-NN Distance and Index Matrices from a Distance Matrix |
-- E --
| edge.diff | Compute Edge Difference Between Two Graphs |
| estimate.geodesic.distances | Estimate Pairwise Geodesic Distances |
| euclidean.distance | Euclidean Distance Between Two Points |
| extract.edge.lengths | Extract Unique Edge Lengths from an Undirected Graph |
| extract.trajectory.edge.lengths | Extract Edge Lengths Along a Graph Path |
-- G --
| generate.circle.graph | Generate a Weighted Circle Graph |
| geodesic.core.endpoints | Select Graph Endpoints by Core-Eccentricity Geometry |
| geodesic.disk | Geodesic Disk in a Weighted Graph |
| geodesic.knn | Estimate Geodesic Nearest Neighbors Within a Point Cloud |
| geodesic.knnx | Estimate Geodesic Nearest Neighbors from Grid Points to Data Points |
| get.edge.weights | Get Unique Edge Weights from a Weighted Graph |
| get.shortest.path | Get Shortest Path Between Two Vertices |
| graph.adj.mat | Convert Coordinates and Edges to a Weighted Adjacency Matrix |
| graph.connected.components | Assign Vertices to Connected Components |
| graph.edit.distance | Calculate Graph Edit Distance (Pure R Implementation) |
| graph.embedding | Embed Graph in 2D or 3D Space |
| graph.geodesic.distances | Compute Graph Geodesic Distances from a Graph Object |
| graph.spectral.embedding | Generate Spectral Embedding of a Graph |
| graph.spectrum | Compute Graph Spectrum |
| graph.summary.divergence | Compute divergence between two graphs using a selected graph summary |
-- I --
| identical.vertex.set.weighted.graph.similarity | Weighted Graph Distance Between Graphs with Identical Vertex Sets |
| isometry.distance.correlations | Compute Distance Preservation Correlations |
| isometry.distortion.quantiles | Compute Multiplicative Distortion Quantiles |
| isometry.geodesic.diagnostics | Compute Geodesic-Isometry Diagnostics |
| isometry.rel.abs.error | Compute Relative Absolute Isometry Errors |
| isometry.rel.rms.error | Compute Relative RMS Isometry Error |
| isometry.scale | Compute the Optimal Isometry Calibration Scale |
-- J --
| jensen.shannon.divergence | Jensen-Shannon Divergence |
| join.graphs | Join Two Adjacency-List Graphs |
-- L --
| load.graph.data | Load Graph Data from RDA Files |
-- M --
| minh.limit | Find the Minimum Hop Limit for Path Existence |
-- N --
| nerve.graph | Construct the Nerve Graph of a Cover |
-- O --
| overlap.distribution.plot | Plot the distribution of overlap values |
-- P --
| path.dist | Normalized Cumulative Distance Along a Vertex Path |
| path.length | Compute Euclidean Path Length |
| plot.build_iknn_graphs_and_selectk | Plot method for build_iknn_graphs_and_selectk |
| plot.cst_graph_mixing_stats | Plot method for cst_graph_mixing_stats |
| plot.geodesic_stats | Plot Geodesic Statistics |
| plot.IkNNgraphs | Plot Diagnostics for Intersection k-NN Graph Analysis |
| plot.iknn_stability_metrics | Plot Method for IkNN Stability Metrics |
| plot.vertex_geodesic_stats | Plot method for vertex_geodesic_stats objects |
| plot2D.colored.graph | Plot a Graph with Colored Vertices |
| print.build_iknn_graphs_and_selectk | Print method for build_iknn_graphs_and_selectk |
| print.geodesic_stats | Print method for geodesic_stats objects |
| print.knn.outliers | Print Method for knn.outliers Objects |
| print.maximal_packing | Print Method for Maximal Packing Results |
| print.mknn_graph | Print Method for mknn_graph Objects |
| print.mknn_graphs | Print Method for mknn_graphs Objects |
| print.mst_completion_graph | Print Method for MST Completion Graph Objects |
| print.packing_validation | Print Method for Packing Validation Results |
| print.summary.knn.outliers | Print Method for summary.knn.outliers Objects |
| print.summary.mst_completion_graph | Print Summary of MST Completion Graph |
-- R --
| remove.knn.outliers | Remove Outliers from a State Space Using k-Nearest Neighbors |
| rm.self.loops | Remove Self-Loops from an Adjacency List |
-- S --
| shortest.path | Computes Shortest Path Distances for Selected Vertices |
| subdivide.path | Subdivide a Path into Arc-Length Spaced Points |
| summarize.isometry.deviation | Summarize Deviation from Isometry |
| summary.geodesic_stats | Summary method for geodesic_stats objects |
| summary.IkNN | Summarize IkNN Graph Object |
| summary.iknn_graphs | Summarize an iknn_graphs Object |
| summary.knn.outliers | Summary Method for knn.outliers Objects |
| summary.mknn_graphs | Summary Method for mknn_graphs Objects |
| summary.mst_completion_graph | Summary Method for MST Completion Graph Objects |
| summary.rknn_graphs | Summarize an rknn_graphs Object |
| summary.vertex_geodesic_stats | Summary method for vertex_geodesic_stats objects |
-- V --
| validate.maximal.packing | Validate a Maximal Packing |
| verify.maximal.packing | Verify Maximal Packing Created by create.maximal.packing |
| vertices | Extract Vertices from a Graph Result |
-- W --
| wgraph.prune.long.edges | Prune Long Edges in a Weighted Graph |