1. 09 Dec, 2020 2 commits
  2. 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
  3. 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
  4. 12 Nov, 2020 1 commit
  5. 09 Nov, 2020 1 commit
  6. 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
  7. 20 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Changes to prediction modules: · baf2ea83
      Chris Jewell authored
      CHANGES:
      
      1. `summary.py` provide a 56 day projection
      2. `medium_term_prediction.py` correct issues turning dates into day, month, year.
      baf2ea83
  8. 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
  9. 01 Oct, 2020 1 commit
    • 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