Package: mappeR 2.0.0

George Clare Kennedy

mappeR: Construct and Visualize TDA Mapper Graphs

Topological data analysis (TDA) is a method of data analysis that uses techniques from topology to analyze high-dimensional data. Here we implement Mapper, an algorithm from this area developed by Singh, Mémoli and Carlsson (2007) which generalizes the concept of a Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.

Authors:George Clare Kennedy [aut, cre]

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mappeR.pdf |mappeR.html✨
mappeR/json (API)
NEWS

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

Bug tracker:https://github.com/uiowa-applied-topology/mapper/issues

On CRAN:

4.16 score 2 stars 16 scripts 663 downloads 9 exports 12 dependencies

Last updated 1 days agofrom:ac44209018. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winOKFeb 17 2025
R-4.5-macOKFeb 17 2025
R-4.5-linuxOKFeb 17 2025
R-4.4-winOKFeb 17 2025
R-4.4-macOKFeb 17 2025
R-4.3-winOKFeb 17 2025
R-4.3-macOKFeb 17 2025

Exports:create_1D_mapper_objectcreate_ball_mapper_objectcreate_ballscreate_clusterball_mapper_objectcreate_mapper_objectcreate_width_balanced_covereccentricity_filterhierarchical_clusterermapper_object_to_igraph

Dependencies:clicpp11fastclusterglueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs

Readme and manuals

Help Manual

Help pageTopics
Construct mapper graph from dataassemble_mapper_object
Get a tester function for an interval.check_in_interval
Compute dispersion of a single clustercompute_tightness
"Clustering" for ballmapper just means treating each bin as its own cluster.convert_to_clusters
Run 1D mappercreate_1D_mapper_object
Run mapper using a trivial filter, a cover of balls, and no clustering algorithm.create_ball_mapper_object
Make a cover of ballscreate_balls
Create bins of datacreate_bins
Run clusterball mappercreate_clusterball_mapper_object
Create a mapper objectcreate_mapper_object
Create a bin of datacreate_single_bin
Generate an overlapping cover of an intervalcreate_width_balanced_cover
Cut a dendrogram in contextcut_dendrogram
Compute eccentricity of data pointseccentricity_filter
Recover binsget_bin_vector
Compute cluster sizesget_cluster_sizes
Compute dispersion measures of a list of clustersget_cluster_tightness_vector
Get data within a clusterget_clustered_data
Perform the clustering step in mapperget_clusters
Calculate edge weightsget_edge_weights
Obtain edge list from cluster intersectionsget_edgelist_from_overlaps
Perform single-linkage hierarchical clustering and process dendrograms in a semi-global context.get_hierarchical_clusters
Get cluster overlapsget_overlaps
Ship data off to the clustering goblinsget_raw_clusters
Find the tallest branch of a dendrogramget_tallest_branch
Create a little dude to perform hierarchical clustering in a semi-global context using the hclust package.hierarchical_clusterer
Get a tester function for a ball.is_in_ball
make igraphmapper_object_to_igraph
Find which triangular number you're onnext_triangular
Cut many dendrograms in contextprocess_dendrograms
Perform agglomerative clustering on a single distance matrix.run_link
Subset a distance matrixsubset_dists