1. 23 Apr, 2021 1 commit
    • Chris Jewell's avatar
      Fix for weekday effect in prediction · 3df0dd34
      Chris Jewell authored
      Previously, when generating forward predictions, the model used the latest value of
      gamma1 for all time points.  This created a prediction artefact depending on what the
      last day of the observed timeseries was.   This is now corrected by projecting the weekday
      forward in time.
      3df0dd34
  2. 16 Mar, 2021 2 commits
  3. 10 Mar, 2021 1 commit
  4. 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
  5. 24 Feb, 2021 1 commit
  6. 02 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 2 commits