1. 15 Feb, 2021 1 commit
  2. 10 Feb, 2021 3 commits
  3. 09 Feb, 2021 1 commit
  4. 08 Feb, 2021 2 commits
  5. 07 Feb, 2021 1 commit
  6. 03 Feb, 2021 2 commits
  7. 02 Feb, 2021 3 commits
  8. 25 Jan, 2021 1 commit
  9. 11 Jan, 2021 3 commits
  10. 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
  11. 08 Jan, 2021 1 commit
  12. 07 Jan, 2021 2 commits
  13. 06 Jan, 2021 3 commits
  14. 05 Jan, 2021 1 commit
  15. 04 Jan, 2021 1 commit
  16. 07 Dec, 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. 09 Nov, 2020 1 commit
  19. 03 Nov, 2020 1 commit
  20. 01 Nov, 2020 1 commit
  21. 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
  22. 22 Oct, 2020 1 commit
  23. 12 Oct, 2020 3 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