1. 15 Apr, 2021 1 commit
  2. 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
  3. 03 Feb, 2021 2 commits
  4. 02 Feb, 2021 2 commits
  5. 25 Jan, 2021 1 commit
  6. 11 Jan, 2021 1 commit
  7. 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
  8. 07 Jan, 2021 1 commit
  9. 06 Jan, 2021 1 commit
  10. 04 Jan, 2021 1 commit
  11. 09 Dec, 2020 1 commit
  12. 07 Dec, 2020 1 commit
  13. 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
  14. 27 Nov, 2020 1 commit
  15. 24 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. 12 Nov, 2020 1 commit
  18. 09 Nov, 2020 1 commit
  19. 03 Nov, 2020 1 commit
  20. 02 Nov, 2020 1 commit
  21. 01 Nov, 2020 1 commit
  22. 27 Oct, 2020 3 commits
    • 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
    • Chris Jewell's avatar
      Updated model spec · b095e844
      Chris Jewell authored
      b095e844
    • Chris Jewell's avatar
      Adjusted for new hierarchical model · d23152c1
      Chris Jewell authored
      d23152c1
  23. 26 Oct, 2020 1 commit
  24. 22 Oct, 2020 3 commits
  25. 03 Oct, 2020 2 commits
  26. 01 Oct, 2020 2 commits
  27. 27 Sep, 2020 2 commits
  28. 25 Sep, 2020 1 commit
    • 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