NEWS.md

In TDApplied: Machine Learning and Inference for Topological Data Analysis

All changes to TDApplied are documented here.

Additions referenced with relevant GitHub Issue or Pull Request number. Please see those for more details.

3.0.4

• fixed distance exponentiation and group permuting in permutation test
• added permutation model inference procedure
• added universal null and enclosing radius functions

3.0.3

• Updated documentation for JOSS paper release

3.0.2

• all CRAN issues for this update were caused by the rho parameter, which invokes external C++ code. We therefore fixed these issues by removing the rho parameter from the predict_diagram_kpca and diagram_distance examples, from all tests and in the ML_and_inference.Rmd file. This parameter has been kept and is still tested, just not tested on CRAN
• sped up the independence_test example by only showing the Gram-matrix approach
• removed warnings from benchmarking plots in Speed.Rmd
• removed dependency on package TDA which is currently unavailable on CRAN

3.0.1

• same updates as 3.0.0 but with more efficient vignette building

3.0.0

• added ability to precompute distance/Gram matrices for ML and inference functions
• added fast approximation to Fisher information metric
• added vignettes for speedups, HCP analysis, personalized analyses and distance calculation comparisons (and removed those parts from the main vignette)
• fixed issues with cv model fitting in diagram_ksvm
• added automatic calculation of t parameters in diagram_ksvm
• decreased memory load on parallel functions (except for permutation test loss function)
• added checks for 0 variance distance matrices in diagram_ksvm
• added comparisons against package rgudhi
• updated DESCRIPTION
• added interpretations tools for vr graphs and multiple representative (co) cycles
• improved HCP analysis
• resolved some distance 0 cases in diagram_distance

2.0.4

• fixed build issues related to use of suggested packages in tests, examples and vignettes

2.0.3

• fixed bootstrap reference in vignette

2.0.2

• set seed in vignette for reproducibility (which is reset at the end)
• added more examples of TDA applications in publications

2.0.1

• increased testing coverage
• fixed issue with th parameter in diagram_kpca
• fixed issue with gamma distribution in independence_test
• added applied analysis of TDApplied on HCP data to package vignette

2.0.0

• added PyH function for fast persistence diagram calculations with python
• added bootstrap_persistence_thresholds for finding "real" topological features in a data set
• added plot_diagram function for plotting persistence diagrams, with or without persistence thresholds
• fixed problem with diagram_distance in which one of the two diagrams was empty in the desired dimension

0.1.3

• fixed small bug with computing mean cv model error for svm
• added tryCatch's around parallelized code to ensure that clusters are closed even when errors occur

0.1.2

• fixed bug with mds test and properly cleaned up parallelization clusters

0.1.1

• Fixed bug with one diagram_mds test, although code was working properly

0.1.0

• Initial version

TDApplied documentation built on Oct. 30, 2024, 9:09 a.m.