1. 02 Feb, 2021 1 commit
  2. 10 Jan, 2021 2 commits
    • Chris Jewell's avatar
      Moved pipeline into covid package directory. · 42f4435f
      Chris Jewell authored
      CHANGES:
      
      1. Committed missing `case_data.py` file
      2. Moved pipeline specification into `covid.ruffus_pipeline`
      3. Moved pipeline initialisation into `covid.pipeline`
      42f4435f
    • Chris Jewell's avatar
      Pipeline bugfixes · 9fe819d7
      Chris Jewell authored
      CHANGES:
      
      1. Replaced `read_phe_cases` with `CasesData`
      2. Column-name fix in `case_exceedance`
      3. Fix column heading in `summarize.infec_incidence`
      4. Add Rt_exceed to `summarize.rt`
      5. Add layer option to `summary_geopackage`
      6. Update `ruffus_pipeline.py` to reflect above changes
      7. Update `template_config.yaml` to reflect above changes
      9fe819d7
  3. 07 Jan, 2021 2 commits
  4. 06 Jan, 2021 1 commit
  5. 04 Jan, 2021 1 commit
  6. 17 Dec, 2020 1 commit
  7. 09 Dec, 2020 1 commit
  8. 07 Dec, 2020 1 commit
  9. 03 Dec, 2020 1 commit
    • Chris Jewell's avatar
      As of analysis 2020-11-30 · 595ea2eb
      Chris Jewell authored
      CHANGES:
      
      1. Re-introduced Tier lockdown covariates.  National lockdown covariate is set to 0 because
         we cannot identify this from the time-varying baseline force of infection.
      
      2. Added inference on variance parameter for the temporal Gaussian process on beta.
      595ea2eb
  10. 19 Nov, 2020 1 commit
    • Chris Jewell's avatar
      Implemented weekday effect for I->R · 107186d1
      Chris Jewell authored
      CHANGES:
      
      1. Implemented log-linear model for weekday effect in I->R hazard;
      2. Updated summary.py and within_between.py to match;
      3. Implemented linear random walk for new gamma0 parameter.
      4. Implemented per-parameter data structure in output HDF5 file.
      107186d1
  11. 09 Nov, 2020 1 commit
  12. 27 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Bug fixes · 18e24dc1
      Chris Jewell authored
      CHANGES:
      
      1. Updated the model to use the new gemlib library;
      2. Removed automatic deletion of results directory by prepare_config.py;
      3. Parameterised `gamma` prior parameters and added to template_config.yaml;
      4. Updated within_between.py to use global configuration file.
      18e24dc1
  13. 26 Oct, 2020 1 commit
  14. 22 Oct, 2020 1 commit
  15. 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
  16. 27 Sep, 2020 1 commit
  17. 29 Jun, 2020 1 commit
  18. 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
  19. 12 Jun, 2020 1 commit
  20. 03 Jun, 2020 1 commit
  21. 01 Jun, 2020 1 commit
  22. 18 May, 2020 1 commit
  23. 12 May, 2020 1 commit
  24. 11 May, 2020 1 commit
  25. 20 Apr, 2020 1 commit
  26. 17 Apr, 2020 1 commit
  27. 09 Apr, 2020 1 commit
  28. 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
  29. 05 Apr, 2020 1 commit
  30. 30 Mar, 2020 2 commits
  31. 28 Mar, 2020 1 commit
  32. 26 Mar, 2020 1 commit
  33. 25 Mar, 2020 1 commit
  34. 22 Mar, 2020 1 commit
  35. 20 Mar, 2020 2 commits
  36. 19 Mar, 2020 1 commit