1. 16 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Bugfix to naming in thin_samples.pkl · 264cea5c
      Chris Jewell authored
      CHANGES:
      
      1. `thin_samples['init_state']` --> `thin_samples['initial_state']`
      2. `thin_samples['events']` --> `thin_samples['seir']`
      3. add time dimension to next generation matrix
      4. update downstream scripts to changes.
      264cea5c
  2. 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
  3. 07 Jan, 2021 1 commit
  4. 06 Jan, 2021 1 commit
  5. 05 Jan, 2021 1 commit
  6. 27 Nov, 2020 1 commit
  7. 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
  8. 09 Nov, 2020 1 commit
  9. 27 Oct, 2020 2 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
      Adjusted for new hierarchical model · d23152c1
      Chris Jewell authored
      d23152c1
  10. 22 Oct, 2020 1 commit