viprs 0.1.2

v0.1.2

on Python PyPI

Changed

• Fixed bug in implementation of .fit method of VIPRS models. Specifically,
  there was an issue with the continued=True flag not working because the OptimizeResult
  object wasn't refreshed.
• Replaced print statements with logging where appropriate (still needs some more work).
• Updated way we measure peak memory in viprs_fit
• Updated dict_concat to just return the element if there's a single entry.
• Refactored pars of VIPRS to cache some recurring computations.
• Updated VIPRSBMA & VIPRSGridSearch to only consider models that
  successfully converged.
• Fixed bug in psuedo_metrics when extracting summary statistics data.
• Streamlined evaluation code.
• Refactored code to slightly reduce import/load time.
• Fixed bug in viprs_evaluate

Added

• Added SNP position to output table from VIPRS objects.
• Added measure of time taken to prepare data in viprs_fit.
• Added option to keep long-range LD regions in viprs_fit.
• Added convergence check based on parameter values.
• Added min_iter parameter to .fit methods to ensure CAVI is run for at least min_iter iterations.
• Added separate method for initializing optimization-related objects.
• Added regularization penalty lambda_min.
• Added Spearman R and residualized R-Squared metrics to continuous metrics.

Additional files

Attached are LD matrices for 6 continental ancestry groups, as defined by the Pan-UKB project. The LD matrices are estimated from unrelated samples in the UK Biobank using block-diagonal masks.