Package: dgraphs 0.3.0.9000

dgraphs: Data-Derived Graph Construction Utilities

Constructs data-derived graphs from numerical observations using mutual, shared-neighbor, intersection, geodesic, radius, adaptive-radius, minimum-spanning-tree completion, and optional iterated adaptive neighborhood methods. Provides graph conversion, pruning, diagnostics, spectral embedding, endpoint detection, and path utilities, with reproducible synthetic geometries and point sampling for graph and embedding experiments. The implemented graph constructions include methods described by Jarvis and Patrick (1973) <doi:10.1109/T-C.1973.223640>, Brito et al. (1997) <doi:10.1016/S0167-7152(96)00213-1>, Berry and Sauer (2019) <doi:10.3934/fods.2019001>, and Gower and Ross (1969) <doi:10.2307/2346439>.

Authors:Pawel Gajer [aut, cre], Sunil Arya [ctb], David M. Mount [ctb], University of Maryland [cph], Yixuan Qiu [ctb, cph], Anna Araslanova [ctb, cph], Gael Guennebaud [ctb, cph], Jitse Niesen [ctb, cph], Netherlands eScience Center [ctb, cph], Danil Kirsanov [ctb, cph]

# Install 'dgraphs' in R:

install.packages('dgraphs', repos = c('https://pgajer.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pgajer/dgraphs/issues

Pkgdown/docs site:https://pgajer.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

6.82 score 1 stars 1 packages 49 scripts 375 downloads 117 exports 16 dependencies

Last updated from:9c17cbea5c. Checks:12 OK, 3 NOTE. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	299
linux-devel-x86_64	OK	326
source / vignettes	OK	467
linux-release-arm64	OK	280
linux-release-x86_64	OK	319
macos-release-arm64	OK	403
macos-release-x86_64	OK	669
macos-oldrel-arm64	NOTE	395
macos-oldrel-x86_64	NOTE	565
windows-devel-arm64	OK	439
windows-devel-x86_64	OK	506
windows-release-arm64	OK	470
windows-release-x86_64	OK	424
windows-oldrel-x86_64	NOTE	374
wasm-release	OK	270

Dependencies:BH cli cpp11 FNN glue igraph lattice lifecycle magrittr Matrix nloptr pkgconfig Rcpp RcppEigen rlang vctrs

Fermat distances and their supporting graphs on surfaces

Rendered fromfermat-surfaces.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-10-01

Density-sensitive paths with Fermat distances

The estimator and its graph restriction | Noisy circles with different sampling densities | Does a sparse graph give the same distances? | Two noisy arms with diffuse background points | How much does the first seed conceal? | Complete-graph distances without storing the graph | Sparse metric MDS with consistent Fermat targets | What the theory does and does not establish | Exact nearest neighbors without all-pairs distances | References

Rendered fromfermat-distances.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-09-30

Finding your way around dgraphs

Rendered fromfunction-guide.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-09-14

IAN graphs: setup and interpreting results

Build the optional backend once | Construct and inspect a graph | Numerical behavior and incomplete results | Resources and qualification

Rendered fromian-graphs.Rmdusingknitr::rmarkdown

Last update: 2026-09-24
Started: 2026-09-24

Synthetic geometry and point sampling

A curve: angles, coordinates and a graph | A quadratic surface: parameter sampling and embedding | Chords, lifted segments and shortest paths | Random frames and single points | Explore quadratic geometry in 3D | Shape: flat, bowl, dome, cylinder, saddle and mixed terms | Sampling: domain, density, gaps and ordering | Placement: canonical, supplied and random frames, with offsets | Dimensions: a curve, multiple heights, a 3D latent domain and one point | Differential geometry: gradient, metric and area element | Inspect the graph and a lifted latent segment | A simplex with a lower-dimensional face | Choosing compatible sampling specifications | Reproducibility and continuation | Opting into the current R stream | Next steps

Rendered fromsynthetic-geometry.Rmdusingknitr::rmarkdown

Last update: 2026-09-15
Started: 2026-09-14

Constructing and Diagnosing Data-Derived Graphs

Rendered fromdata-derived-graph-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2026-08-21

Help page	Topics
dgraphs: Data-Derived Graph Construction Utilities	dgraphs-package dgraphs
Convert a dgraph to igraph	as_igraph
Build the Optional IAN Backend	build.ian.backend
Build iKNN Graphs and Select a Neighborhood Size	build.iknn.graphs.and.selectk
Compare Two Adjacency Lists	compare.adj.lists
Compare Paths Across Hop Limits	compare.paths
Compute Geodesic Statistics for Grid Vertices	compute.geodesic.stats
Compute a Weighted Graph Diameter	compute.graph.diameter
Compute a Weighted Shortest-Path Distance	compute.graph.distance
Compute Graph Endpoint Scores from a 3D Embedding	compute.graph.endpoint.scores
Compute a graph summary as a probability mass function	compute.graph.summary.pmf
Compute graph-summary stability across a graph sequence	compute.graph.summary.stability
Compute Stability Metrics Across a Sequence of IkNN Graphs	compute.stability.metrics
Compute Geodesic Statistics for a Single Grid Vertex	compute.vertex.geodesic.stats
Convert an Adjacency List to an Adjacency Matrix	convert.adjacency.list.to.adjacency.matrix
Convert an Adjacency List to an Edge Matrix	convert.adjacency.to.edge.matrix
Convert a Directed Adjacency List to an Undirected Adjacency List	convert.to.undirected
Convert a Weighted Adjacency Matrix to Lists	convert.weighted.adjacency.matrix.to.adjacency.list
Count Edges in an Undirected Adjacency List	count.edges
Compute a Continuous-kNN Graph	create.cknn.graph
Construct a Minimal Spanning Tree (MST) Completion Graph	create.cmst.graph
Create a graph-geodesic iKNN graph	create.geodesic.iknn.graph
Create a Standard Graph	create.graph
Create a Refined Graph with Approximately Uniform Edge Spacing	create.grid.graph
Construct an Iterated Adaptive Neighborhood Graph	create.ian.graph
Create intersection k-nearest neighbor graphs with dual pruning	create.iknn.graphs
Create iterated graph-geodesic iKNN graphs	create.iterated.iknn.graphs
Create a Maximal Packing of Vertices in a Graph	create.maximal.packing
Compute a Mutual k-Nearest Neighbor Graph with Weights	create.mknn.graph
Create Multiple Mutual kNN Graphs with Geometric Pruning	create.mknn.graphs
Construct Path Graphs Across Hop Limits	create.path.graph
Create a Path Length Matrix Graph Structure	create.plm.graph
Compute a Radius-kNN Graph	create.rknn.graph
Compute Adaptive Radius-kNN Graphs Across k Values	create.rknn.graphs
Create a Single Intersection-weighted k-Nearest Neighbors Graph	create.single.iknn.graph
Compute a Symmetric k-Nearest Neighbor Graph	create.sknn.graph
Compute a Series of Symmetric k-Nearest Neighbor Graphs	create.sknn.graphs
Extract an Induced Subgraph	create.subgraph
Create a Threshold Distance Graph	create.threshold.distance.graph
Detect Graph Endpoints from a 3D Embedding	detect.graph.endpoints
Detect Local Extrema in a Graph	detect.local.extrema
Construct and Inspect an Undirected Metric Graph	dgraph graph.adjacency graph.edge.attribute graph.edges graph.lengths graph.order graph.stages
Compute Edge Difference Between Two Graphs	edge.diff
Exact latent-segment lengths under a synthetic geometry	edge.lengths.synthetic.geometry
Lift coordinates onto a quadratic surface using Geometry Lab arithmetic	embed.quadform.surface
Embed latent coordinates through a synthetic geometry	embed.synthetic.geometry
Open the Graph Reconstruction Explorer	explore.graphs
Extract Edge Lengths Along a Graph Path	extract.trajectory.edge.lengths
Compute Complete or Graph-Restricted Sample Fermat Distances	fermat.distances
Find Exact Sample Fermat Nearest Neighbors	create.fermat.sknn.graph fermat.knn
Select Graph Endpoints by Core-Eccentricity Geometry	geodesic.core.endpoints
Geodesic Disk in a Weighted Graph	geodesic.disk
Find Geodesic Neighbors Within a Point Cloud	geodesic.knn
Find Geodesic Neighbors from Grid Queries to Observations	geodesic.knnx
Get Shortest Path Between Two Vertices	get.shortest.path
Assign Vertices to Connected Components	graph.connected.components
Embed Graph in 2D or 3D Space	graph.embedding
Compute Graph Geodesic Distances	graph.geodesic.distances
Embed a Connected Graph Using its Positive Laplacian Spectrum	graph.spectral.embedding
Compute the Positive Spectrum of an Unweighted Graph Laplacian	graph.spectrum
Compute divergence between two graphs using a selected graph summary	graph.summary.divergence
Weighted Graph Distance Between Graphs with Identical Vertex Sets	identical.vertex.set.weighted.graph.similarity
Inspect a Path Graph	inspect.path.graph print.path.graph summary.path.graph
Inspect a Collection of Hop-Constrained Path Graphs	inspect.path.graph.series print.path.graph.series summary.path.graph.series
Inspect a Synthetic Geometry Sample	inspect.synthetic_geometry_sample print.summary.synthetic_geometry_sample print.synthetic_geometry_sample summary.synthetic_geometry_sample
Compute Distance Preservation Correlations	isometry.distance.correlations
Compute Multiplicative Distortion Quantiles	isometry.distortion.quantiles
Compute Geodesic-Isometry Diagnostics	isometry.geodesic.diagnostics
Compute Relative Absolute Isometry Errors	isometry.rel.abs.error
Compute Relative RMS Isometry Error	isometry.rel.rms.error
Compute the Optimal Isometry Calibration Scale	isometry.scale
Jensen-Shannon Divergence	jensen.shannon.divergence
Join Two Adjacency-List Graphs	join.graphs
Find the Minimum Hop Limit for Path Existence	minh.limit
Construct the Nerve Graph of a Cover	nerve.graph
Plot the distribution of overlap values	overlap.distribution.plot
Normalized Cumulative Distance Along a Vertex Path	path.dist
Compute Euclidean Path Length	path.length
Plot method for build_iknn_graphs_and_selectk	plot.build_iknn_graphs_and_selectk
Plot method for cst_graph_mixing_stats	plot.cst_graph_mixing_stats
Plot a dgraph with Reusable Coordinates	plot.dgraph
Plot Geodesic Statistics	plot.geodesic_stats
Plot Method for IkNN Stability Metrics	plot.iknn_stability_metrics
Plot Diagnostics for Intersection k-NN Graph Analysis	plot.IkNNgraphs
Plot method for vertex_geodesic_stats objects	plot.vertex_geodesic_stats
Print method for build_iknn_graphs_and_selectk	print.build_iknn_graphs_and_selectk
Print an Undirected Graph	print.dgraph
Print method for geodesic_stats objects	print.geodesic_stats
Print Graph Constructor Results	print.adaptive_radius_graph print.cknn_graph print.graph.constructors print.radius_graph print.rknn_graphs print.sknn_graph print.sknn_graphs
Print Method for knn.outliers Objects	print.knn.outliers
Print Method for Maximal Packing Results	print.maximal_packing
Print Method for mknn_graph Objects	print.mknn_graph
Print Method for mknn_graphs Objects	print.mknn_graphs
Print Method for MST Completion Graph Objects	print.mst_completion_graph
Print Method for Packing Validation Results	print.packing_validation
Print a Path-Length-Metric Graph	print.path.graph.plm
Print Method for summary.knn.outliers Objects	print.summary.knn.outliers
Print Summary of MST Completion Graph	print.summary.mst_completion_graph
Evaluate gradients of all quadforms	quadform.gradient
Evaluate the induced metric of a quadform geometry	quadform.metric
Read a Saved Graph Reconstruction Benchmark	read.graph.benchmark
Remember a Graph Explorer Project	register.graph.project
Remove Outliers from a State Space Using k-Nearest Neighbors	remove.knn.outliers
Remove Self-Loops from an Adjacency List	rm.self.loops
Realize points on a synthetic geometry with explicit random-state control	sample.synthetic.geometry
Subdivide a Path into Arc-Length Spaced Points	subdivide.path
Summarize Deviation from Isometry	summarize.isometry.deviation
Summary method for geodesic_stats objects	summary.geodesic_stats
Summarize IkNN Graph Object	summary.IkNN
Summarize an iknn_graphs Object	summary.iknn_graphs
Summarize Iterated Intersection k-NN Graphs	summary.iterated_iknn_graphs
Summary Method for knn.outliers Objects	summary.knn.outliers
Summarize Local Extrema	print.summary.local_extrema summary.local_extrema
Summary Method for mknn_graphs Objects	summary.mknn_graphs
Summary Method for MST Completion Graph Objects	summary.mst_completion_graph
Summarize an rknn_graphs Object	summary.rknn_graphs
Summary method for vertex_geodesic_stats objects	summary.vertex_geodesic_stats
Specify a circle geometry	synthetic.circle
Specify a helix geometry	synthetic.helix
Specify a point-line junction	synthetic.point.line.junction
Specify a quadform geometry	synthetic.quadform
Clustered sampling specification	synthetic.sampling.clustered
Dirichlet sampling with structural zeros	synthetic.sampling.dirichlet.zeros
Gapped-uniform sampling specification	synthetic.sampling.gapped.uniform
Deterministic interval-grid sampling specification	synthetic.sampling.grid.interval
Versioned quadratic-surface sampling used by Geometry Lab	synthetic.sampling.quadform.lab
Truncated-normal sampling specification	synthetic.sampling.truncated.normal
Uniform-box sampling specification	synthetic.sampling.uniform.box
Uniform-disk sampling specification	synthetic.sampling.uniform.disk
Uniform-interval sampling specification	synthetic.sampling.uniform.interval
Uniform-rectangle sampling specification	synthetic.sampling.uniform.rectangle
Specify a simplex geometry	synthetic.simplex
Specify a sphere-cap geometry	synthetic.sphere.cap
Assemble a stratified geometry	synthetic.stratified
Specify a point stratum	synthetic.stratum.point
Specify a rectangle stratum	synthetic.stratum.rectangle
Specify a line-segment stratum	synthetic.stratum.segment
Specify a torus-patch geometry	synthetic.torus.patch
Specify a trefoil-knot geometry	synthetic.trefoil
Validate a Maximal Packing	validate.maximal.packing
Validate a geometry specification or its latent coordinates	validate.synthetic.geometry
Validate a point-sampling specification and geometric support	validate.synthetic.sampling
Verify Maximal Packing Created by create.maximal.packing	verify.maximal.packing
Extract Vertices from a Graph Result	vertices
Extract a Local-Extremum Neighborhood	vertices.local_extrema
Prune Long Edges in a Weighted Graph	wgraph.prune.long.edges

Package: dgraphs 0.3.0.9000

dgraphs: Data-Derived Graph Construction Utilities

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