- 23 Apr, 2021 3 commits
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Chris Jewell authored
Investigation showed that the high rate of cases in the UK in January caused a significant discretisation error between the chain binomial model and continuous time analogues. The previous Rt calculation made use of a continuous time approximation, and so gave biased estimates of Rt. The new implementation calculates Rt using expectations of the chain binomial model in terms of transition probabilities, not rates as previously.
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Chris Jewell authored
Fix for weekday effect in prediction See merge request !37
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Chris Jewell authored
Previously, when generating forward predictions, the model used the latest value of gamma1 for all time points. This created a prediction artefact depending on what the last day of the observed timeseries was. This is now corrected by projecting the weekday forward in time.
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- 20 Apr, 2021 1 commit
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Chris Jewell authored
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- 15 Apr, 2021 1 commit
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Chris Jewell authored
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- 14 Apr, 2021 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 11 Apr, 2021 2 commits
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Chris Jewell authored
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Chris Jewell authored
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- 30 Mar, 2021 2 commits
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Chris Jewell authored
Fix to trap ChunkedEncodingError in data download See merge request !36
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Chris Jewell authored
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- 24 Mar, 2021 5 commits
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Chris Jewell authored
Fix download retry See merge request !35
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Chris Jewell authored
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Chris Jewell authored
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Chris Jewell authored
Add option to push to AWS buckets See merge request !34
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Chris Jewell authored
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- 21 Mar, 2021 1 commit
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Chris Jewell authored
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- 20 Mar, 2021 1 commit
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Chris Jewell authored
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- 18 Mar, 2021 1 commit
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Chris Jewell authored
CHANGES: 1. Add option to upload results to AWS S3 bucket 2. Remove generation of insample plots from pipeline
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- 17 Mar, 2021 3 commits
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Chris Jewell authored
Modified Rt calculation See merge request !33
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Chris Jewell authored
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Chris Jewell authored
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- 16 Mar, 2021 5 commits
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Chris Jewell authored
CHANGES: 1. The posterior NGM is now not saved, only the sum over all destinations to give $R_{it}$ 2. Replace Rt as the dominant eigenvalue of the NGM with weighted average by population size. 3. ngm.nc now contains both $R_{it}$ and $R_t$ posterior predictive values.
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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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Chris Jewell authored
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Chris Jewell authored
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Chris Jewell authored
This reverts commit 53f6937b
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- 15 Mar, 2021 1 commit
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Chris Jewell authored
Regular TF graph mode appears to be faster for the current code implementation.
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- 10 Mar, 2021 1 commit
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Chris Jewell authored
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- 06 Mar, 2021 4 commits
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Chris Jewell authored
Adjusted pipeline to ensure config.yaml is written to results dir first. See merge request !32
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Chris Jewell authored
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Chris Jewell authored
Fix geopackage geometry joining issue See merge request !31
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Chris Jewell authored
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- 05 Mar, 2021 1 commit
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Chris Jewell authored
Use xarray/netCDF4 throughout the pipeline See merge request !30
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- 04 Mar, 2021 5 commits
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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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Chris Jewell authored
Added cumulative incidence to `summary_longformat.xlsx` See merge request !29
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Chris Jewell authored
CHANGES: 1. Added code in `summary_longformat.py` to calculate cumulative incidence; 2. Switched from `openpyxl` to `xlsxwriter` for lower memory usage when writing to summary_longformat.xlsx.
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Chris Jewell authored
Added daily absolute incidence and incidence per 100k to summary_longformat.py See merge request !28
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Chris Jewell authored
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- 03 Mar, 2021 1 commit
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Chris Jewell authored
Added insample7 summary to summary_longformat.xlsx See merge request !27
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