Changelog

0.3.0 - 2026-09-08

  • Added follow-up end-date checks to medical-record processing and corrected invalid-record summaries.

  • Made disease-covariate adjustment in trajectory analyses time-aware to prevent the use of future diagnoses.

  • Updated the Phecode mapping and information .npy files to correct exclusion definitions.

  • Required each participant’s end date to be later than their index date.

  • Improved automatic classification of categorical and continuous covariates.

  • Removed incomplete medical records before diagnosis-code processing.

  • Standardized ICD codes before exclusion filtering and Phecode mapping.

  • Corrected sex-specific disease filtering in PheWAS.

  • Excluded participants with invalid follow-up periods before PheWAS summaries, thresholds, and model fitting.

  • Calculated proportional PheWAS thresholds from each disease-eligible population.

  • Corrected the relative-risk and phi-coefficient significance tests, including boundary handling for phi values of 1.

  • Restricted disease-pair construction to serial execution to prevent inconsistent results.

  • Corrected RPCN fitting when a user-specified penalty is provided.

  • Corrected automatic scaling of the RPCN penalty.

  • Corrected handling of custom relative-risk significance columns.

  • Applied temporal-order settings consistently across analysis stages.

  • Validated that trajectory and comorbidity results contain matching disease pairs.

  • Harmonized pipeline execution modes and recorded the selected stage order.

  • Calculated proportional comorbidity-strength thresholds from each disease-pair-eligible population.

0.2.0 - 2026-08-29

  • Added Plot.interactive_website() for generating self-contained offline websites from available PheWAS, comorbidity-network, disease-trajectory, and 3D network results.

0.1.17 - 2026-08-26

  • Added method and maxiter parameters to phewas() for configuring the statsmodels Cox optimizer.

  • Fixed forwarding of method-specific RPCN and PCN-PCA parameters in disease_network_pipeline().

  • Updated the analysis API documentation to distinguish the PheWAS optimizer method from the pipeline network-analysis method.

0.1.15 - 2026-07-23

  • enhance convergence warning handling in Cox model functions.

0.1.14 - 2026-05-09

  • Fixed inconsistent module assignments across comorbidity, trajectory, and 3D network plots when both comorbidity and trajectory results are provided.

  • Improved multiprocessing stability for PheWAS, comorbidity network, and disease trajectory model-fitting steps on Linux servers.

  • Added multiprocessing_start_method support for model-fitting steps and improved progress reporting for parallel runs.

0.1.13 - 2026-03-30

  • Updated the Plot module so PheWAS, comorbidity, and trajectory plots can be created with only the result tables each plot type requires.

0.1.12 - 2026-03-11

  • Fixed a bug in the visualization module.

  • Added the get_louvain_clusters function to the visualization module.

  • Improved the wording and clarity of medical record summary text.

0.1.11 - 2026-02-11

  • Fixed a failure in compute_vif_sm_exact when multi-column dependency issues were encountered.

0.1.10 - 2025-12-09

  • Added the ability to highlight connected edges when a node is clicked in the 3D figure.

0.1.9 - 2025-11-13

  • Fixed incorrect parameter descriptions in the visualization module.

0.1.8 - 2025-10-23

  • Fixed a bug in the visualization module.

0.1.7 - 2025-10-15

  • Added the correct node legend to the comorbidity network plot.

  • Updated phecode system labels in the plots.

0.1.6 - 2025-10-06

  • Fixed several bugs in the visualization module.

0.1.5 - 2025-10-04

  • Added support for phecode version 1.3a.

0.1.4 - 2025-10-02

  • Fixed a bug in the comorbidity network estimation step that could produce imaginary numbers in the phi correlation.

0.1.3 - 2025-08-28

  • Fixed a bug in visualization.py.

0.1.0 - 2025-08-13

  • First stable version released.