1. 23 Apr, 2021 1 commit
    • Chris Jewell's avatar
      Change to Rt calculation to fix discretisation error · 35f04b91
      Chris Jewell authored
      Investigation showed that the high rate of cases in the UK in January
      caused a significant discretisation error between the chain binomial
      model and continuous time analogues.  The previous Rt calculation
      made use of a continuous time approximation, and so gave biased
      estimates of Rt.
      
      The new implementation calculates Rt using expectations of the chain
      binomial model in terms of transition probabilities, not rates as
      previously.
      35f04b91
  2. 15 Apr, 2021 1 commit
  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. 03 Feb, 2021 2 commits
  5. 02 Feb, 2021 2 commits
  6. 25 Jan, 2021 1 commit
  7. 11 Jan, 2021 1 commit
  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. 07 Jan, 2021 1 commit
  10. 06 Jan, 2021 1 commit
  11. 04 Jan, 2021 1 commit
  12. 09 Dec, 2020 1 commit
  13. 07 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. 24 Nov, 2020 1 commit
  17. 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
  18. 12 Nov, 2020 1 commit
  19. 09 Nov, 2020 1 commit
  20. 03 Nov, 2020 1 commit
  21. 02 Nov, 2020 1 commit
  22. 01 Nov, 2020 1 commit
  23. 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
  24. 26 Oct, 2020 1 commit
  25. 22 Oct, 2020 3 commits
  26. 03 Oct, 2020 2 commits
  27. 01 Oct, 2020 2 commits
  28. 27 Sep, 2020 2 commits
  29. 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