NEWS
TDApplied 3.0.4 (2024-10-29)
- fixed distance exponentiation and group permuting in permutation test
- added permutation model inference procedure
- added universal null and enclosing radius functions
TDApplied 3.0.3 (2024-03-12)
- Updated documentation for JOSS paper release
TDApplied 3.0.2 (2024-01-21)
- 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
TDApplied 3.0.1
- same updates as 3.0.0 but with more efficient vignette building
TDApplied 3.0.0 (2023-12-07)
- 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
TDApplied 2.0.4 (2023-01-25)
- fixed build issues related to use of suggested packages in tests, examples and vignettes
TDApplied 2.0.3 (2023-01-15)
- fixed bootstrap reference in vignette
TDApplied 2.0.2 (2023-01-12)
- set seed in vignette for reproducibility (which is reset at the end)
- added more examples of TDA applications in publications
TDApplied 2.0.1 (2022-12-23)
- 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
TDApplied 2.0.0 (2022-11-08)
- 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
TDApplied 0.1.3 (2022-10-02)
- 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
TDApplied 0.1.2 (2022-09-26)
- fixed bug with mds test and properly cleaned up parallelization clusters
TDApplied 0.1.1 (2022-08-29)
- Fixed bug with one diagram_mds test, although code was working properly
TDApplied 0.1.0 (2022-08-15)