- 14 Apr, 2021 1 commit
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Chris Jewell authored
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- 16 Mar, 2021 1 commit
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Chris Jewell authored
CHANGES: 1. `thin_samples['init_state']` --> `thin_samples['initial_state']` 2. `thin_samples['events']` --> `thin_samples['seir']` 3. add time dimension to next generation matrix 4. update downstream scripts to changes.
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- 04 Mar, 2021 1 commit
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Chris Jewell authored
CHANGES 1. Most tasks touched to use netCDF4 inferencedata file. 2. Added netCDF4 metadata copy to covid.util 3. Updated model_spec.py to use xarray 4. Updated covid.ruffus_pipeline to use netCDF4 files, adding pipeline metadata 5. Updated pyproject.toml 6. Removed chunk specification in inference.py. Defer to automatic chunking for now.
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- 15 Feb, 2021 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 02 Feb, 2021 1 commit
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Chris Jewell authored
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- 25 Jan, 2021 1 commit
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Chris Jewell authored
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- 11 Jan, 2021 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 10 Jan, 2021 1 commit
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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
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- 08 Jan, 2021 1 commit
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Chris Jewell authored
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- 07 Jan, 2021 1 commit
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Chris Jewell authored
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- 06 Jan, 2021 1 commit
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Chris Jewell authored
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- 04 Jan, 2021 1 commit
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Chris Jewell authored
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- 09 Dec, 2020 1 commit
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Chris Jewell authored
Note: in the actual analysis, the effect of December Tiers was removed.
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- 03 Dec, 2020 1 commit
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Chris Jewell authored
CHANGES: 1. Re-introduced Tier lockdown covariates. National lockdown covariate is set to 0 because we cannot identify this from the time-varying baseline force of infection. 2. Added inference on variance parameter for the temporal Gaussian process on beta.
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- 27 Nov, 2020 1 commit
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Chris Jewell authored
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- 19 Nov, 2020 1 commit
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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.
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- 09 Nov, 2020 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 08 Nov, 2020 1 commit
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Chris Jewell authored
CHANGES: 1. Re-implemented trace_fn 2. Implemented new Posterior class in `gemlib`
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- 03 Nov, 2020 1 commit
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Chris Jewell authored
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- 02 Nov, 2020 1 commit
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Chris Jewell authored
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- 01 Nov, 2020 1 commit
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Chris Jewell authored
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- 26 Oct, 2020 1 commit
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Chris Jewell authored
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- 22 Oct, 2020 5 commits
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Chris Jewell authored
MCMC update kernels in `interface.py` changed to reflect new AdaptiveRandomWalkMetropolis interface.
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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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Chris Jewell authored
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- 05 Oct, 2020 1 commit
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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.
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- 03 Oct, 2020 4 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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Chris Jewell authored
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- 01 Oct, 2020 2 commits
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Chris Jewell authored
CHANGES: 1. Added `data/example_cases.py`, `data/uk_clip.py`, `covid/summary.py`, `summary.py` 2. `summary.py` computes summary values required by reports to SAGE 3. Small changes to `inference.py` and `simulate.py` to reflect baked-in `nu` parameter in `model_spec.py`.
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Chris Jewell authored
Removed redundant code from `inference.py` (duplicated in `model_spec.py`). Small change to `xi_freq` parameter in `model_spec.py`.
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- 27 Sep, 2020 1 commit
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Chris Jewell authored
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- 25 Sep, 2020 2 commits
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Chris Jewell authored
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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.
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