1. 14 Apr, 2021 1 commit
  2. 16 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Bugfix to naming in thin_samples.pkl · 264cea5c
      Chris Jewell authored
      CHANGES:
      
      1. `thin_samples['init_state']` --> `thin_samples['initial_state']`
      2. `thin_samples['events']` --> `thin_samples['seir']`
      3. add time dimension to next generation matrix
      4. update downstream scripts to changes.
      264cea5c
  3. 04 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Use xarray/netCDF4 throughout the pipeline · 023cbc5f
      Chris Jewell authored
      CHANGES
      
      1. Most tasks touched to use netCDF4 inferencedata file.
      2. Added netCDF4 metadata copy to covid.util
      3. Updated model_spec.py to use xarray
      4. Updated covid.ruffus_pipeline to use netCDF4 files, adding pipeline metadata
      5. Updated pyproject.toml
      6. Removed chunk specification in inference.py.  Defer to automatic chunking for now.
      023cbc5f
  4. 15 Feb, 2021 2 commits
  5. 02 Feb, 2021 1 commit
  6. 25 Jan, 2021 1 commit
  7. 11 Jan, 2021 2 commits
  8. 10 Jan, 2021 1 commit
    • 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
  9. 08 Jan, 2021 1 commit
  10. 07 Jan, 2021 1 commit
  11. 06 Jan, 2021 1 commit
  12. 04 Jan, 2021 1 commit
  13. 09 Dec, 2020 1 commit
  14. 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
  15. 27 Nov, 2020 1 commit
  16. 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
  17. 09 Nov, 2020 2 commits
  18. 08 Nov, 2020 1 commit
  19. 03 Nov, 2020 1 commit
  20. 02 Nov, 2020 1 commit
  21. 01 Nov, 2020 1 commit
  22. 26 Oct, 2020 1 commit
  23. 22 Oct, 2020 5 commits
  24. 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
  25. 03 Oct, 2020 4 commits
  26. 01 Oct, 2020 2 commits
  27. 27 Sep, 2020 1 commit
  28. 25 Sep, 2020 2 commits
    • Chris Jewell's avatar
      Code tidy. · d247c771
      Chris Jewell authored
      d247c771
    • Chris Jewell's avatar
      Refactored model specification · e52283b6
      Chris Jewell authored
      Changes:
      
      1. Created a TFP JointDistribution to represent full probability model;
      2. Renamed CovidUKStochastic --> DiscreteTimeStateTransitionModel;
      3. DiscreteTimeStateTransitionModel now inherits from tfp.Distribution.
      e52283b6