1. 08 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Adaptive Hamiltonian Monte Carlo within Gibbs implementation · 1676ca5d
      Chris Jewell authored
      CHANGES:
      
      1. Kernel builder functions moved to `mcmc_kernel_factory.py`
      2. Windowed adaptive MCMC a la STAN implemented in `inference.py`
      3. Prior on beta1 tightened to improve stability.
      4. Depends on `gemlib`@develop branch for tf-nightly and tfp-nightly
      1676ca5d
  2. 24 Feb, 2021 3 commits
  3. 17 Feb, 2021 1 commit
  4. 15 Feb, 2021 2 commits
  5. 10 Feb, 2021 3 commits
  6. 09 Feb, 2021 1 commit
  7. 08 Feb, 2021 2 commits
  8. 07 Feb, 2021 1 commit
  9. 03 Feb, 2021 2 commits
  10. 02 Feb, 2021 3 commits
  11. 25 Jan, 2021 1 commit
  12. 11 Jan, 2021 3 commits
  13. 10 Jan, 2021 4 commits
    • Chris Jewell's avatar
      Minor bugfixes · 8423f467
      Chris Jewell authored
      8423f467
    • Chris Jewell's avatar
      Moved pipeline into covid package directory. · 42f4435f
      Chris Jewell authored
      CHANGES:
      
      1. Committed missing `case_data.py` file
      2. Moved pipeline specification into `covid.ruffus_pipeline`
      3. Moved pipeline initialisation into `covid.pipeline`
      42f4435f
    • Chris Jewell's avatar
      Addition of insample posterior check plots · 80bbe105
      Chris Jewell authored
      80bbe105
    • 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
  14. 08 Jan, 2021 1 commit
  15. 07 Jan, 2021 2 commits
  16. 06 Jan, 2021 3 commits
  17. 05 Jan, 2021 1 commit
  18. 04 Jan, 2021 1 commit
  19. 07 Dec, 2020 1 commit
  20. 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
  21. 09 Nov, 2020 1 commit
  22. 03 Nov, 2020 1 commit
  23. 01 Nov, 2020 1 commit