as_igraph               Convert a dgraph to igraph
build.ian.backend       Build the Optional IAN Backend
build.iknn.graphs.and.selectk
                        Build iKNN Graphs and Select a Neighborhood
                        Size
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.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
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-package         dgraphs: Data-Derived Graph Construction
                        Utilities
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
fermat.distances        Compute Complete or Graph-Restricted Sample
                        Fermat Distances
fermat.knn              Find Exact Sample Fermat Nearest Neighbors
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.connected.components
                        Assign Vertices to Connected Components
graph.embedding         Embed Graph in 2D or 3D Space
graph.geodesic.distances
                        Compute Graph Geodesic Distances
graph.spectral.embedding
                        Embed a Connected Graph Using its Positive
                        Laplacian Spectrum
graph.spectrum          Compute the Positive Spectrum of an Unweighted
                        Graph Laplacian
graph.summary.divergence
                        Compute divergence between two graphs using a
                        selected graph summary
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
jensen.shannon.divergence
                        Jensen-Shannon Divergence
join.graphs             Join Two Adjacency-List Graphs
linf.simplex.distances
                        Intrinsic Euclidean distances on the
                        nonnegative L-infinity simplex
minh.limit              Find the Minimum Hop Limit for Path Existence
nerve.graph             Construct the Nerve Graph of a Cover
overlap.distribution.plot
                        Plot the distribution of overlap values
path.dist               Normalized Cumulative Distance Along a Vertex
                        Path
path.length             Compute Euclidean Path Length
plot.IkNNgraphs         Plot Diagnostics for Intersection k-NN Graph
                        Analysis
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.iknn_stability_metrics
                        Plot Method for IkNN Stability Metrics
plot.vertex_geodesic_stats
                        Plot method for vertex_geodesic_stats objects
print.build_iknn_graphs_and_selectk
                        Print method for build_iknn_graphs_and_selectk
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.plm    Print a Path-Length-Metric Graph
print.summary.knn.outliers
                        Print Method for summary.knn.outliers Objects
print.summary.mst_completion_graph
                        Print Summary of MST Completion Graph
quadform.gradient       Evaluate gradients of all quadforms
quadform.metric         Evaluate the induced metric of a quadform
                        geometry
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
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.IkNN            Summarize IkNN Graph Object
summary.geodesic_stats
                        Summary method for geodesic_stats objects
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.rknn_graphs     Summarize an rknn_graphs Object
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
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
wgraph.prune.long.edges
                        Prune Long Edges in a Weighted Graph
