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