1. 16 Mar, 2021 2 commits
    • Chris Jewell's avatar
      Add time axis to Rt · 215a0ee0
      Chris Jewell authored
      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.
    • Chris Jewell's avatar
      Bugfix to naming in thin_samples.pkl · 264cea5c
      Chris Jewell authored
      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.
  2. 04 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Use xarray/netCDF4 throughout the pipeline · 023cbc5f
      Chris Jewell authored
      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.
  3. 24 Feb, 2021 1 commit
  4. 07 Jan, 2021 1 commit