stephenslab / flashr

R package for Empirical Bayes Factor Analysis.
https://stephenslab.github.io/flashr
BSD 3-Clause "New" or "Revised" License
49 stars 11 forks source link

Re-factoring, improved verbose output, warmstart, handle LL and fixl #75

Closed willwerscheid closed 6 years ago

willwerscheid commented 6 years ago

Major re-factoring, including eliminating r1_opt so that we reuse code and we let backfitting use the good things we did to speed up flash_add_greedy (another advantage is that parallelizing the backfit is now possible). Improved verbose output and moved to separate file. Moved nullcheck to separate file and re-organized flash, updates, and r1_opt. Added warmstart functionality and made it default for ebnm_pn. Added handling functions for add_fixed (fixes #71 ).

codecov-io commented 6 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@e31c415). Click here to learn what that means. The diff coverage is 91.07%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master      #75   +/-   ##
=========================================
  Coverage          ?   85.05%           
=========================================
  Files             ?       17           
  Lines             ?     1017           
  Branches          ?        0           
=========================================
  Hits              ?      865           
  Misses            ?      152           
  Partials          ?        0
Impacted Files Coverage Δ
R/flash_data.R 86.66% <ø> (ø)
R/updates.R 100% <100%> (ø)
R/objective.R 100% <100%> (ø)
R/flash_add.R 100% <100%> (ø)
R/nullcheck.R 100% <100%> (ø)
R/flash.R 90.9% <100%> (ø)
R/update_precision.R 86.2% <100%> (ø)
R/get_functions.R 75.43% <38.46%> (ø)
R/r1_opt.R 77.19% <76.92%> (ø)
R/handle_params.R 83.76% <78.94%> (ø)
... and 3 more

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