Package: SimplicialComplex 0.2.1

ChiChien Wang

SimplicialComplex: Topological Data Analysis: Simplicial Complex

Provides an implementation of simplicial complexes for Topological Data Analysis (TDA). The package includes functions to compute faces, boundary operators, Betti numbers, Euler characteristic, and to construct simplicial complexes, including Vietoris-Rips, Cech, Alpha, Delaunay, Witness, flood, and (via a Freudenthal triangulation) cubical complexes for grid and image data. It also implements persistent homology, from building filtrations (via a single build_filtration() entry point covering all of the above) to computing persistence diagrams, persistence landscapes, and Wasserstein/bottleneck distances between diagrams, with the aim of helping readers understand the core concepts of computational topology. Methods are based on standard references in persistent homology such as Zomorodian and Carlsson (2005) <doi:10.1007/s00454-004-1146-y>, Chazal and Michel (2021) <doi:10.3389/frai.2021.667963>, and Otter, Porter, Tillmann, Grindrod and Harrington (2017) <doi:10.1140/epjds/s13688-017-0109-5>.

Authors:ChiChien Wang [aut, cre, trl]

SimplicialComplex_0.2.1.tar.gz
SimplicialComplex_0.2.1.zip(r-4.7-any)SimplicialComplex_0.2.1.zip(r-4.6-any)SimplicialComplex_0.2.1.zip(r-4.5-any)
SimplicialComplex_0.2.1.tgz(r-4.6-any)SimplicialComplex_0.2.1.tgz(r-4.5-any)
SimplicialComplex_0.2.1.tar.gz(r-4.7-any)SimplicialComplex_0.2.1.tar.gz(r-4.6-any)
SimplicialComplex_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SimplicialComplex/json (API)

# Install 'SimplicialComplex' in R:
install.packages('SimplicialComplex', repos = c('https://tda-r.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tda-r/simplicialcomplex/issues

On CRAN:

Conda:

4.35 score 5 stars 1 scripts 261 downloads 43 exports 34 dependencies

Last updated from:c39c7ad449. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK179
source / vignettesOK200
macos-releaseOK217
macos-oldrelOK193
windows-develOK113
windows-releaseOK113

Exports:AlphaComplexas_filtrationbetti_numberbottleneck_distanceboundaryboundary_infobuild_cubical_filtrationbuild_filtrationbuild_flood_filtrationCechComplexcollect_gcompare_complexescomplex_distancecrockerDelaunayComplexdiagram_matchingeuler_characteristicextract_persistence_pairsfacesflood_complexflood_persistencegauss_jordan_eliminategenerate_landmarkshomologyimkerlower_star_filtrationmorse_reconpartial_pers_dmvfpersistence_landscapepersistence_pairsplot_crockerplot_landscapeplot_matchingplot_morse_landscapeplot_morse_reconplot_morse_vpathplot_persistencerestrict_filtrationVietorisRipsComplexwasserstein_distanceWitnessComplexzigzag_persistence

Dependencies:abindcliclueclustercpp11farvergeometryggplot2gluegtablegtoolsigraphisobandlabelinglatticelifecyclelinproglpSolvemagicmagrittrMASSMatrixpkgconfigR6RANNRColorBrewerRcppRcppProgressrlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Construct an Alpha ComplexAlphaComplex
Convert a flood_complex object to a filtration listas_filtration
Bottleneck distance between two persistence diagramsbottleneck_distance
Compute the boundary operator for a simplicial complexboundary
Get the boundary matrix and its reduction information in matrix formboundary_info
Build a cubical (grid) filtration from an imagebuild_cubical_filtration
Build a filtration from a point cloud, for any of five complex typesbuild_filtration
Flood filtration in SimplicialComplex formatbuild_flood_filtration
Construct a Cech ComplexCechComplex
Collect 1-unstable manifolds into a reconstructed graphcollect_g
Compare simplicial complex constructions on one point cloudcompare_complexes
Wasserstein/bottleneck distance between two point clouds, via one chosen complexcomplex_distance
Compute a CROCKER matrix for a time-varying point cloudcrocker
Construct a Delaunay ComplexDelaunayComplex
Optimal point matching between two persistence diagramsdiagram_matching
Compute the Euler characteristic chi of a simplicial complexeuler_characteristic
This function extracts the persistence from combining the boundary matrix and its filtrationextract_persistence_pairs
Generate all unique faces of a given dimension from simplicesfaces
Construct a Flood complexflood_complex
Persistence pairs via sparse boundary reductionflood_persistence
Row-reduce (partial pivoting) a matrixgauss_jordan_eliminate
Farthest-Point Sampling of landmarksgenerate_landmarks
Basic graph Laplacian L = D - Agraph_laplacian
Ordinary Hodge Laplacianhodge_laplacian
Compute a homology basis from a cycle basis and a boundary basishomology
Compute a basis for the image (column space) of a matrixim
Compute a basis for the kernel (null space) of a matrixker
Generalizes 'build_cubical_filtration' to any triangulation: given the maximal simplices of a simplicial complex and a function defined at its vertices, builds the simplex-wise lower-star filtration \mathcal{F}_f.lower_star_filtration
Reconstruct a hidden graph from a density fieldmorse_recon
Persistence-guided discrete Morse vector field on a graph (1-complex)partial_pers_dmvf
Compute the persistence landscape of a persistence diagrampersistence_landscape
Persistence pairs via sparse boundary reduction (for large filtrations)persistence_pairs
Persistent (combinatorial) Laplacianpersistent_laplacian
Plot a CROCKER matrix as a filled contour plotplot_crocker
Plot a Persistence Landscapeplot_landscape
Plot the optimal matching between two persistence diagramsplot_matching
Plot the density landscape and critical structure in interactive 3Dplot_morse_landscape
Plot the graph reconstructed by 'morse_recon'plot_morse_recon
Plot a local patch of the triangulation with its discrete gradient fieldplot_morse_vpath
Plot Persistence Diagramplot_persistence
Restrict a filtration list to simplices up to a given dimensionrestrict_filtration
Construct a Vietoris–Rips Complex (1-skeleton + maximal simplices)VietorisRipsComplex
Wasserstein distance between two persistence diagramswasserstein_distance
Construct a Witness ComplexWitnessComplex
Compute the persistence barcode of a zigzag filtration of simplicial complexeszigzag_persistence