Package: TDApplied 3.0.4

TDApplied: Machine Learning and Inference for Topological Data Analysis

Topological data analysis is a powerful tool for finding non-linear global structure in whole datasets. The main tool of topological data analysis is persistent homology, which computes a topological shape descriptor of a dataset called a persistence diagram. 'TDApplied' provides useful and efficient methods for analyzing groups of persistence diagrams with machine learning and statistical inference, and these functions can also interface with other data science packages to form flexible and integrated topological data analysis pipelines.

Authors:Shael Brown [aut, cre], Dr. Reza Farivar [aut, fnd]

TDApplied_3.0.4.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
TDApplied/json (API)
NEWS

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

Bug tracker:https://github.com/shaelebrown/tdapplied/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.65 score 18 stars 9 scripts 610 downloads 23 exports 11 dependencies

Last updated from:1283762615. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK306
linux-devel-x86_64OK304
source / vignettesOK360
linux-release-arm64OK278
linux-release-x86_64OK300
macos-release-arm64OK196
macos-release-x86_64OK429
macos-oldrel-arm64OK203
macos-oldrel-x86_64OK471
windows-develOK257
windows-releaseOK275
windows-oldrelOK284
wasm-releaseOK155

Exports:bootstrap_persistence_thresholdsdiagram_distancediagram_kerneldiagram_kkmeansdiagram_kpcadiagram_ksvmdiagram_mdsdiagram_to_dfdistance_matrixenclosing_radiusgram_matriximport_ripserindependence_testpermutation_model_inferencepermutation_testplot_diagramplot_vr_graphpredict_diagram_kkmeanspredict_diagram_kpcapredict_diagram_ksvmPyHuniversal_nullvr_graphs

Dependencies:clueclustercodetoolsdoParallelforeachiteratorskernlabparallellyRcppRcppArmadillordist

Benchmarking and Speedups

Shael Brown and Dr. Reza Farivar

Rendered fromSpeed.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2024-01-01
Started: 2023-02-14

Comparing Distance Calculations

Shael Brown and Dr. Reza Farivar

Rendered fromcomparing_calcs.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2023-04-27
Started: 2023-04-05

Human Connectome Project Analysis

Shael Brown and Dr. Reza Farivar

Rendered fromHCP_analysis.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2023-12-10
Started: 2023-02-14

Personalized Analyses with TDApplied

Shael Brown and Dr. Reza Farivar

Rendered frompersonalized_analyses.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2023-04-25
Started: 2023-04-04

TDApplied Theory and Practice

Shael Brown and Dr. Reza Farivar

Rendered fromML_and_Inference.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2024-10-23
Started: 2022-03-30

Readme and manuals

Help Manual

Help pageTopics
Analyze the data point memberships of multiple representative (co)cycles.analyze_representatives
Estimate persistence threshold(s) for topological features in a data set using bootstrapping.bootstrap_persistence_thresholds
Make sure that python has been configured correctly for persistent homology calculations.check_PyH_setup
Verify an imported ripser module.check_ripser
Calculate distance between a pair of persistence diagrams.diagram_distance
Calculate persistence Fisher kernel value between a pair of persistence diagrams.diagram_kernel
Cluster a group of persistence diagrams using kernel k-means.diagram_kkmeans
Calculate the kernel PCA embedding of a group of persistence diagrams.diagram_kpca
Fit a support vector machine model where each training set instance is a persistence diagram.diagram_ksvm
Dimension reduction of a group of persistence diagrams via metric multidimensional scaling.diagram_mds
Convert a TDA/TDAstats persistence diagram to a data frame.diagram_to_df
Compute a distance matrix from a list of persistence diagrams.distance_matrix
Compute the enclosing radius for a dataset.enclosing_radius
Compute the gram matrix for a group of persistence diagrams.gram_matrix
Import the python module ripser.import_ripser
Independence test for two groups of persistence diagrams.independence_test
Model inference with permutation test.permutation_model_inference
Permutation test for finding group differences between persistence diagrams.permutation_test
Plot persistence diagramsplot_diagram
Plot a VR graph using the igraph package.plot_vr_graph
Predict the cluster labels for new persistence diagrams using a pre-computed clustering.predict_diagram_kkmeans
Project persistence diagrams into a low-dimensional space via a pre-computed kernel PCA embedding.predict_diagram_kpca
Predict the outcome labels for a list of persistence diagrams using a pre-trained diagram ksvm model.predict_diagram_ksvm
Fast persistent homology calculations with python.PyH
Filtering topological features with the universal null distribution.universal_null
Compute Vietoris-Rips graphs of a dataset at particular epsilon radius values.vr_graphs