1. 10 Jan, 2021 3 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
      Addition of insample posterior check plots · 80bbe105
      Chris Jewell authored
      80bbe105
    • 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
  2. 08 Jan, 2021 1 commit
  3. 07 Jan, 2021 4 commits
  4. 06 Jan, 2021 6 commits
  5. 05 Jan, 2021 4 commits
  6. 04 Jan, 2021 3 commits
  7. 17 Dec, 2020 1 commit
  8. 09 Dec, 2020 4 commits
  9. 07 Dec, 2020 1 commit
  10. 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
  11. 27 Nov, 2020 1 commit
  12. 24 Nov, 2020 1 commit
  13. 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
  14. 12 Nov, 2020 4 commits
  15. 09 Nov, 2020 4 commits
  16. 08 Nov, 2020 1 commit