1. 16 Mar, 2021 2 commits
    • Chris Jewell's avatar
      Add time axis to Rt · 215a0ee0
      Chris Jewell authored
      CHANGES:
      
      1. The posterior NGM is now not saved, only the sum over all destinations to give $R_{it}$
      2. Replace Rt as the dominant eigenvalue of the NGM with weighted average by population size.
      3. ngm.nc now contains both $R_{it}$ and $R_t$ posterior predictive values.
      215a0ee0
    • 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. 24 Feb, 2021 1 commit
  4. 10 Feb, 2021 1 commit
  5. 09 Feb, 2021 1 commit
  6. 08 Feb, 2021 2 commits
  7. 10 Jan, 2021 1 commit
    • 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
  8. 07 Jan, 2021 1 commit