1. 22 Oct, 2020 1 commit
  2. 06 Oct, 2020 1 commit
  3. 05 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Major new pipelining structure · bfcaf904
      Chris Jewell authored
      ==============================
      
      enqueue_pipeline.sh --> covid_pipeline.sge --> prepare_config.py --> inference.py --> summary.py
      
      enqueue_pipeline.sh identifies the dataset and analysis period, launching 4 SGE jobs [P1, P1+2]\times[specimen_date, report_date]
      
      Each SGE job runs the inference and summary scripts, using information contained in a config.yaml file.
      
      The config.yaml file, together with results outputs, are stored in a results directory specified the config file
      and over-ridden in the top-level enqueue_pipeline.sh script.
      bfcaf904
  4. 27 Sep, 2020 1 commit
  5. 29 Jun, 2020 1 commit
  6. 24 Jun, 2020 1 commit
    • Chris Jewell's avatar
      Changes: · e72cfe76
      Chris Jewell authored
      1. Formatting -- black style!
      2. After profiling, implemented a better workaround for the
      tfd.Categorical bug.  Replaced with an inherited Categorical2 class,
      with overloaded log_prob function.
      3. Fixed a  bug in EventTimeProposal where tfd.FiniteDiscrete was
      being used on a non-strictly-increasing outcomes vector.
      4. Increased number of meta-populations to 149 to mirror UK UTLA regions.
      e72cfe76
  7. 12 Jun, 2020 1 commit
  8. 03 Jun, 2020 1 commit
  9. 01 Jun, 2020 1 commit
  10. 18 May, 2020 1 commit
  11. 12 May, 2020 1 commit
  12. 11 May, 2020 1 commit
  13. 20 Apr, 2020 1 commit
  14. 17 Apr, 2020 1 commit
  15. 09 Apr, 2020 1 commit
  16. 08 Apr, 2020 1 commit
    • Chris Jewell's avatar
      Major changes: · 94fe710d
      Chris Jewell authored
      1. chainbinom* file and methods renamed to discrete_markov* files and methods.
      
      2. Implemented batched hazard rate calculation, adding functions to automatically broadcast rates to the Markov transition rate matrix.
      
      3. Implemented test simulation and MCMC algorithm.
      94fe710d
  17. 05 Apr, 2020 1 commit
  18. 30 Mar, 2020 2 commits
  19. 28 Mar, 2020 1 commit
  20. 26 Mar, 2020 1 commit
  21. 25 Mar, 2020 1 commit
  22. 22 Mar, 2020 1 commit
  23. 20 Mar, 2020 2 commits
  24. 19 Mar, 2020 1 commit
  25. 16 Mar, 2020 1 commit
  26. 15 Mar, 2020 1 commit
  27. 12 Mar, 2020 1 commit
  28. 08 Mar, 2020 1 commit
  29. 03 Mar, 2020 1 commit