1. 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
  2. 09 Nov, 2020 2 commits
  3. 08 Nov, 2020 1 commit
  4. 03 Nov, 2020 1 commit
  5. 02 Nov, 2020 1 commit
  6. 01 Nov, 2020 1 commit
  7. 26 Oct, 2020 1 commit
  8. 22 Oct, 2020 5 commits
  9. 05 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Major new pipelining structure · bfcaf904
      Chris Jewell authored
      ==============================
      
      enqueue_pipeline.sh --> covid_pipeline.sge --> prepare_config.py --> inference.py --> summary.py
      
      enqueue_pipeline.sh identifies the dataset and analysis period, launching 4 SGE jobs [P1, P1+2]\times[specimen_date, report_date]
      
      Each SGE job runs the inference and summary scripts, using information contained in a config.yaml file.
      
      The config.yaml file, together with results outputs, are stored in a results directory specified the config file
      and over-ridden in the top-level enqueue_pipeline.sh script.
      bfcaf904
  10. 03 Oct, 2020 2 commits
  11. 01 Oct, 2020 2 commits
  12. 27 Sep, 2020 1 commit
  13. 25 Sep, 2020 2 commits
    • Chris Jewell's avatar
      Code tidy. · d247c771
      Chris Jewell authored
      d247c771
    • Chris Jewell's avatar
      Refactored model specification · e52283b6
      Chris Jewell authored
      Changes:
      
      1. Created a TFP JointDistribution to represent full probability model;
      2. Renamed CovidUKStochastic --> DiscreteTimeStateTransitionModel;
      3. DiscreteTimeStateTransitionModel now inherits from tfp.Distribution.
      e52283b6
  14. 23 Sep, 2020 1 commit
  15. 11 Sep, 2020 1 commit
  16. 05 Sep, 2020 1 commit
  17. 04 Sep, 2020 1 commit
    • Chris Jewell's avatar
      Pulled dates out of CovidUKStochastic class · 588d479e
      Chris Jewell authored
      Changes:
      
      1. Dates are pulled out of CovidUKStochastic
      2. CovidUKStochastic now behaves more like a tfd.Distribution
          * CovidUKStochastic is now instantiated with an initial time, number of time steps and
      time step size
          * CovidUKStochastic is now instantiated with the initial state.
      588d479e
  18. 30 Aug, 2020 1 commit
    • Chris Jewell's avatar
      Corrected Add/Delete move bounds. · 71205807
      Chris Jewell authored
      Consider an SEIR model.  For adding $x \geq 0$ S->E event times we have:
      \begin{equation}
      S(t+1) &=& S(0) - (N_{se}(t) + x) \geq 0 \\
      E(t+1) &=& E(0) + (N_{se}(t) + x) \geq 0
      \end{equation}
      such that $x$ is bounded by
      $$
      x \leq S(0) - N_{se}(t).
      $$
      
      Similarly for adding $x \geq 0$ E->I event times we have:
      $$
      x \leq E(0) + N_{se}(t) - N_{ei}(t).
      $$
      
      For deleting $x \geq 0$ S->E event times we have:
      $$
      x \leq E(0) + N_{se}(t) - N_{ei}(t)
      $$
      and for E->I event times we have;
      $$
      x \leq I(0) + N_{ei}(t) - N_{ir}(t).
      $$
      71205807
  19. 28 Aug, 2020 1 commit
  20. 26 Aug, 2020 2 commits
  21. 23 Aug, 2020 1 commit
    • Chris Jewell's avatar
      Corrected data misalignment · 2d0e3f80
      Chris Jewell authored
      Changes:
      
      1. We adopt the convention [start, end) for *all* date ranges.
      2. Modified PHE case ingestor to reflect this
      3. Modified CovidUK to reflect this
      4. Corrected a bug in the use of time in simulation.
      2d0e3f80
  22. 20 Aug, 2020 1 commit
  23. 17 Aug, 2020 1 commit
  24. 16 Aug, 2020 2 commits
  25. 08 Aug, 2020 1 commit
  26. 07 Aug, 2020 2 commits
    • Chris Jewell's avatar
      Implemented nested Gibbs sampling · b8a89f41
      Chris Jewell authored
      b8a89f41
    • Chris Jewell's avatar
      Implemented kernel-ised Gibbs sampler · 7adf0699
      Chris Jewell authored
      Changes:
      
      1. Implemented GibbsStep and GibbsKernel classes
      2. Modified mcmc.sample function to use Gibbs sampler
      3. Amended bugs in event_time_mh.py and occult_proposal.py (edge cases where tf.gathers
      were overshooting the bounds of the data stuctures, not apparent on a GPU but raised on
      CPU).
      7adf0699
  27. 01 Aug, 2020 2 commits
  28. 30 Jul, 2020 1 commit