CHANGES:

1. Add option to upload results to AWS S3 bucket
2. Remove generation of insample plots from pipeline

Modified Rt calculation

See merge request !33

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.

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.

This reverts commit 53f6937b

Regular TF graph mode appears to be faster for the current code
implementation.

CHANGES:

1. Size of posterior dataset is calculated automatically;
2. Require `num_adaptation_iterations` in config file;
3. Set progress bar to measure iterations.

CHANGES:

1. Kernel builder functions moved to `mcmc_kernel_factory.py`
2. Windowed adaptive MCMC a la STAN implemented in `inference.py`
3. Prior on beta1 tightened to improve stability.
4. Depends on `gemlib`@develop branch for tf-nightly and tfp-nightly

Adjusted pipeline to ensure config.yaml is written to results dir first.

See merge request !32

Fix geopackage geometry joining issue

See merge request !31

Use xarray/netCDF4 throughout the pipeline

See merge request !30

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.

Added cumulative incidence to `summary_longformat.xlsx`

See merge request !29

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.

Added daily absolute incidence and incidence per 100k to summary_longformat.py

See merge request !28

Added insample7 summary to summary_longformat.xlsx

See merge request !27

Weekly 100k

See merge request !26

Switched to NetCDF4 storage of predictive output

See merge request !25

Chris Jewell authored Feb 24, 2021 and Chris Jewell committed Feb 24, 2021

Changes:

1. Where xarrays were pickled to disc, we now use xarray.to_netcdf
2. Where xarrays were read from Python pickles, we now use xarray.load_dataset


(cherry picked from commit 63519eb3)