1. 03 Oct, 2020 1 commit
  2. 01 Oct, 2020 2 commits
  3. 27 Sep, 2020 1 commit
  4. 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
  5. 23 Sep, 2020 1 commit
  6. 11 Sep, 2020 1 commit
  7. 05 Sep, 2020 1 commit
  8. 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
  9. 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
  10. 28 Aug, 2020 1 commit
  11. 26 Aug, 2020 2 commits
  12. 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
  13. 20 Aug, 2020 1 commit
  14. 17 Aug, 2020 1 commit
  15. 16 Aug, 2020 2 commits
  16. 08 Aug, 2020 1 commit
  17. 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
  18. 01 Aug, 2020 2 commits
  19. 30 Jul, 2020 1 commit
  20. 24 Jul, 2020 1 commit
  21. 22 Jul, 2020 1 commit
    • Chris Jewell's avatar
      Implemented LTLA-level COVID-19 model · 68b27bba
      Chris Jewell authored
      Changes:
      
      1. Replaced 149 UTLAs with 315 LTLAs mixing matrix;
      2. Wrote geometric initialisation for censored event times;
      3. Modified data ingester to take PHE Anonymised Line Listing data.
      68b27bba
  22. 09 Jul, 2020 1 commit
  23. 08 Jul, 2020 1 commit
    • Chris Jewell's avatar
      Added occult inference capability · cad36259
      Chris Jewell authored
      Changes:
      
      1. Added occult Metropolis Hastings update.
      2. Factored out Categorical2 distribution for use by both event time move and occults.
      3. Refactored mcmc.py script for HDF5 output purposes
      4. Apply compression to HDF5 output file.
      cad36259
  24. 05 Jul, 2020 3 commits
  25. 04 Jul, 2020 2 commits
  26. 29 Jun, 2020 1 commit
  27. 28 Jun, 2020 3 commits
  28. 27 Jun, 2020 2 commits