1. 02 Feb, 2021 1 commit
  2. 25 Jan, 2021 1 commit
  3. 11 Jan, 2021 3 commits
  4. 10 Jan, 2021 4 commits
    • Chris Jewell's avatar
      Minor bugfixes · 8423f467
      Chris Jewell authored
      8423f467
    • 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
  5. 08 Jan, 2021 1 commit
  6. 07 Jan, 2021 2 commits
  7. 06 Jan, 2021 3 commits
  8. 05 Jan, 2021 1 commit
  9. 04 Jan, 2021 1 commit
  10. 07 Dec, 2020 1 commit
  11. 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
  12. 09 Nov, 2020 1 commit
  13. 03 Nov, 2020 1 commit
  14. 01 Nov, 2020 1 commit
  15. 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
  16. 22 Oct, 2020 1 commit
  17. 12 Oct, 2020 1 commit
  18. 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
  19. 04 Oct, 2020 1 commit
  20. 03 Oct, 2020 1 commit
  21. 01 Oct, 2020 2 commits
    • Chris Jewell's avatar
      Minor changes · 6900b230
      Chris Jewell authored
      1. removed redundant code from `covid/summary.py`
      2. added to README
      6900b230
    • Chris Jewell's avatar
      Added inference summary metrics · 8eb0ab69
      Chris Jewell authored
      CHANGES:
      
      1. Added `data/example_cases.py`, `data/uk_clip.py`, `covid/summary.py`, `summary.py`
      2. `summary.py` computes summary values required by reports to SAGE
      3. Small changes to `inference.py` and `simulate.py` to reflect baked-in `nu` parameter in `model_spec.py`.
      8eb0ab69
  22. 27 Sep, 2020 1 commit
  23. 26 Sep, 2020 1 commit
  24. 25 Sep, 2020 3 commits
  25. 24 Sep, 2020 1 commit
  26. 23 Sep, 2020 1 commit
  27. 21 Sep, 2020 1 commit
  28. 16 Sep, 2020 1 commit
  29. 14 Sep, 2020 1 commit