# Data-Derived Graph Construction Utilities

## Documentation for package ‘dgraphs’ version 0.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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