- 24 Sep, 2020 1 commit
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Chris Jewell authored
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- 23 Sep, 2020 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 22 Sep, 2020 1 commit
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Chris Jewell authored
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- 21 Sep, 2020 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 16 Sep, 2020 1 commit
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Chris Jewell authored
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- 14 Sep, 2020 4 commits
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Chris Jewell authored
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Chris Jewell authored
Includes specified US style date format.
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Chris Jewell authored
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Chris Jewell authored
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- 11 Sep, 2020 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 05 Sep, 2020 1 commit
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Chris Jewell authored
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- 04 Sep, 2020 1 commit
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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.
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- 30 Aug, 2020 3 commits
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Chris Jewell authored
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Chris Jewell authored
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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; $$ x \leq I(0) + N_{ei}(t) - N_{ir}(t). $$
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- 28 Aug, 2020 1 commit
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Chris Jewell authored
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- 26 Aug, 2020 2 commits
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Chris Jewell authored
Changes: 1. Previously, we initialised from the first imputed event at T-s, where s was random due to the initialisation process; 2. We now calculate the state at time T given s (and the event imputation).
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Chris Jewell authored
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- 23 Aug, 2020 1 commit
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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.
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- 20 Aug, 2020 3 commits
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Chris Jewell authored
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Chris Jewell authored
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Chris Jewell authored
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- 17 Aug, 2020 1 commit
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Chris Jewell authored
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- 16 Aug, 2020 2 commits
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Chris Jewell authored
Introduced counting process respecting AddOccultsProposal. This now check to make sure we don't invalidate the epidemic by adding too many events. To achieve this, we combine occults and POEs into 1 structure. This has the advantage of requiring less storage, but is less easy to monitor occults separately from POEs.
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Chris Jewell authored
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- 14 Aug, 2020 3 commits
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Chris Jewell authored
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Chris Jewell authored
Added simple kernel wrapper for fixing parts of the cahin without having to modify the chain output code.
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Chris Jewell authored
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- 12 Aug, 2020 1 commit
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Chris Jewell authored
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- 09 Aug, 2020 4 commits
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Chris Jewell authored
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Chris Jewell authored
Changes: 1. Implemented unittest 2. Removed tf.print statement
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Chris Jewell authored
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Chris Jewell authored
When initiating occults from a previous posterior sample, it is often necessary to make sure that the strict ordering of events is adhered to. `regularize_occults` performs a recursive adjustment of the occults to ensure that strict ordering remains intact.
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- 08 Aug, 2020 1 commit
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Chris Jewell authored
Changes: 1. Bounded convergence parameter mis-specified in samplers (was 0.0, now 1.0) 2. Added 'name' property to GibbsStep
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- 07 Aug, 2020 2 commits
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Chris Jewell authored
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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).
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- 06 Aug, 2020 1 commit
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Chris Jewell authored
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