1. 24 Sep, 2020 1 commit
  2. 23 Sep, 2020 2 commits
  3. 22 Sep, 2020 1 commit
  4. 21 Sep, 2020 2 commits
  5. 16 Sep, 2020 1 commit
  6. 14 Sep, 2020 4 commits
  7. 11 Sep, 2020 2 commits
  8. 05 Sep, 2020 1 commit
  9. 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
  10. 30 Aug, 2020 3 commits
    • Chris Jewell's avatar
      2d1895bf
    • Chris Jewell's avatar
      8a870d29
    • 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
  11. 28 Aug, 2020 1 commit
  12. 26 Aug, 2020 2 commits
  13. 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
  14. 20 Aug, 2020 3 commits
  15. 17 Aug, 2020 1 commit
  16. 16 Aug, 2020 2 commits
  17. 14 Aug, 2020 3 commits
  18. 12 Aug, 2020 1 commit
  19. 09 Aug, 2020 4 commits
  20. 08 Aug, 2020 1 commit
  21. 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
  22. 06 Aug, 2020 1 commit