Commit bd5ca69d authored by Chris Jewell's avatar Chris Jewell
Browse files

Added inference documentation.

parent 21bef411
......@@ -14,6 +14,32 @@ implementing an ETL step, the model itself, and associated inference and predict
Users requiring an end-to-end pipeline implementation should refer to the [covid-pipeline](https://github.com/chrism0dwk/covid-pipeline)
repository.
For development users, the recommended package management system is [`poetry`](https://python-poetry.org). Follow the instructions in the `poetry` documentation to install it.
From a `bash`-like command line, clone the `covid19uk` repo and install dependencies
```bash
git clone <path to this repo>
cd covid19uk
poetry install
```
To run the various algorithms, a general configuration file must be specified, as exemplified in `example_config.yaml` which runs the model on a month's worth of publicly available COVID19 case data from the 11 Northern Irish Local Authority Districts. The configuration file specifies the location of raw data, which we assemble into a NetCDF4 file:
```bash
mkdir results
poetry run python -m covid19uk.data.assemble example_config.yaml results/inferencedata.nc
```
The inference algorithm may then be run using the assembled data
```bash
poetry run python -m covid19uk.inference.inference \
-c example_config.yaml \
-o results/posterior.hd5 \
inferencedata.nc
```
The resulting HDF5 file `results/posterior.hd5` contains the posterior samples.
## COVID-19 Lancaster University data statement
......
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