Data-Derived Graph Construction Utilities

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Documentation for package ‘dgraphs’ version 0.4.0

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A B C D E F G I J L M N O P Q R S V W

dgraphs-package dgraphs: Data-Derived Graph Construction Utilities

-- A --

as_igraph Convert a dgraph to igraph

-- B --

build.ian.backend Build the Optional IAN Backend
build.iknn.graphs.and.selectk Build iKNN Graphs and Select a Neighborhood Size

-- C --

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
create.cknn.graph Compute a Continuous-kNN Graph
create.cmst.graph Construct a Minimal Spanning Tree (MST) Completion Graph
create.fermat.sknn.graph Find Exact Sample Fermat Nearest Neighbors
create.geodesic.iknn.graph Create a graph-geodesic iKNN graph
create.graph Create a Standard Graph
create.grid.graph Create a Refined Graph with Approximately Uniform Edge Spacing
create.ian.graph Construct an Iterated Adaptive Neighborhood Graph
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 Construct Path Graphs Across Hop Limits
create.plm.graph Create a Path Length Matrix Graph Structure
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.sknn.graphs Compute a Series of Symmetric k-Nearest Neighbor Graphs
create.subgraph Extract an Induced Subgraph
create.threshold.distance.graph Create a Threshold Distance Graph

-- D --

detect.graph.endpoints Detect Graph Endpoints from a 3D Embedding
detect.local.extrema Detect Local Extrema in a Graph
dgraph Construct and Inspect an Undirected Metric Graph
dgraphs dgraphs: Data-Derived Graph Construction Utilities

-- E --

edge.diff Compute Edge Difference Between Two Graphs
edge.lengths.synthetic.geometry Exact latent-segment lengths under a synthetic geometry
embed.quadform.surface Lift coordinates onto a quadratic surface using Geometry Lab arithmetic
embed.synthetic.geometry Embed latent coordinates through a synthetic geometry
explore.graphs Open the Graph Reconstruction Explorer
extract.trajectory.edge.lengths Extract Edge Lengths Along a Graph Path

-- F --

fermat.distances Compute Complete or Graph-Restricted Sample Fermat Distances
fermat.knn Find Exact Sample Fermat Nearest Neighbors

-- G --

geodesic.core.endpoints Select Graph Endpoints by Core-Eccentricity Geometry
geodesic.disk Geodesic Disk in a Weighted Graph
geodesic.knn Find Geodesic Neighbors Within a Point Cloud
geodesic.knnx Find Geodesic Neighbors from Grid Queries to Observations
get.shortest.path Get Shortest Path Between Two Vertices
graph.adjacency Construct and Inspect an Undirected Metric Graph
graph.connected.components Assign Vertices to Connected Components
graph.edge.attribute Construct and Inspect an Undirected Metric Graph
graph.edges Construct and Inspect an Undirected Metric Graph
graph.embedding Embed Graph in 2D or 3D Space
graph.geodesic.distances Compute Graph Geodesic Distances
graph.lengths Construct and Inspect an Undirected Metric Graph
graph.order Construct and Inspect an Undirected Metric Graph
graph.spectral.embedding Embed a Connected Graph Using its Positive Laplacian Spectrum
graph.spectrum Compute the Positive Spectrum of an Unweighted Graph Laplacian
graph.stages Construct and Inspect an Undirected Metric Graph
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
inspect.path.graph Inspect a Path Graph
inspect.path.graph.series Inspect a Collection of Hop-Constrained Path Graphs
inspect.synthetic_geometry_sample Inspect a Synthetic Geometry Sample
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 --

linf.simplex.distances Intrinsic Euclidean distances on the nonnegative L-infinity simplex

-- 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.dgraph Plot a dgraph with Reusable Coordinates
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
print.adaptive_radius_graph Print Graph Constructor Results
print.build_iknn_graphs_and_selectk Print method for build_iknn_graphs_and_selectk
print.cknn_graph Print Graph Constructor Results
print.dgraph Print an Undirected Graph
print.geodesic_stats Print method for geodesic_stats objects
print.graph.constructors Print Graph Constructor Results
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.path.graph Inspect a Path Graph
print.path.graph.plm Print a Path-Length-Metric Graph
print.path.graph.series Inspect a Collection of Hop-Constrained Path Graphs
print.radius_graph Print Graph Constructor Results
print.rknn_graphs Print Graph Constructor Results
print.sknn_graph Print Graph Constructor Results
print.sknn_graphs Print Graph Constructor Results
print.summary.knn.outliers Print Method for summary.knn.outliers Objects
print.summary.local_extrema Summarize Local Extrema
print.summary.mst_completion_graph Print Summary of MST Completion Graph
print.summary.synthetic_geometry_sample Inspect a Synthetic Geometry Sample
print.synthetic_geometry_sample Inspect a Synthetic Geometry Sample

-- Q --

quadform.gradient Evaluate gradients of all quadforms
quadform.metric Evaluate the induced metric of a quadform geometry

-- R --

read.graph.benchmark Read a Saved Graph Reconstruction Benchmark
register.graph.project Remember a Graph Explorer Project
remove.knn.outliers Remove Outliers from a State Space Using k-Nearest Neighbors
rm.self.loops Remove Self-Loops from an Adjacency List

-- S --

sample.synthetic.geometry Realize points on a synthetic geometry with explicit random-state control
shortest.path Compute shortest-path distances from legacy adjacency lists
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.iterated_iknn_graphs Summarize Iterated Intersection k-NN Graphs
summary.knn.outliers Summary Method for knn.outliers Objects
summary.local_extrema Summarize Local Extrema
summary.mknn_graphs Summary Method for mknn_graphs Objects
summary.mst_completion_graph Summary Method for MST Completion Graph Objects
summary.path.graph Inspect a Path Graph
summary.path.graph.series Inspect a Collection of Hop-Constrained Path Graphs
summary.rknn_graphs Summarize an rknn_graphs Object
summary.synthetic_geometry_sample Inspect a Synthetic Geometry Sample
summary.vertex_geodesic_stats Summary method for vertex_geodesic_stats objects
synthetic.circle Specify a circle geometry
synthetic.helix Specify a helix geometry
synthetic.point.line.junction Specify a point-line junction
synthetic.quadform Specify a quadform geometry
synthetic.sampling.clustered Clustered sampling specification
synthetic.sampling.dirichlet.zeros Dirichlet sampling with structural zeros
synthetic.sampling.gapped.uniform Gapped-uniform sampling specification
synthetic.sampling.grid.interval Deterministic interval-grid sampling specification
synthetic.sampling.quadform.lab Versioned quadratic-surface sampling used by Geometry Lab
synthetic.sampling.truncated.normal Truncated-normal sampling specification
synthetic.sampling.uniform.box Uniform-box sampling specification
synthetic.sampling.uniform.disk Uniform-disk sampling specification
synthetic.sampling.uniform.interval Uniform-interval sampling specification
synthetic.sampling.uniform.rectangle Uniform-rectangle sampling specification
synthetic.simplex Specify a simplex geometry
synthetic.sphere.cap Specify a sphere-cap geometry
synthetic.stratified Assemble a stratified geometry
synthetic.stratum.point Specify a point stratum
synthetic.stratum.rectangle Specify a rectangle stratum
synthetic.stratum.segment Specify a line-segment stratum
synthetic.torus.patch Specify a torus-patch geometry
synthetic.trefoil Specify a trefoil-knot geometry

-- V --

validate.maximal.packing Validate a Maximal Packing
validate.synthetic.geometry Validate a geometry specification or its latent coordinates
validate.synthetic.sampling Validate a point-sampling specification and geometric support
verify.maximal.packing Verify Maximal Packing Created by create.maximal.packing
vertices Extract Vertices from a Graph Result
vertices.local_extrema Extract a Local-Extremum Neighborhood

-- W --

wgraph.prune.long.edges Prune Long Edges in a Weighted Graph