EpiPI

General Information

This package consists of scripts to run inference of incidecnes on each day based on the prevalence data generated from the sampling. This repository has a Jupyter Notebook file summarising work can be done with this package, which is in the file work_summary.ipynb.

Installation

Currently, EpiPI is only tested on MacOS and Linux. Windows are not supported at the moment.

Installation of EpiPI depends on the CPU of the machine that you are using.

For x86 CPU:

EpiPI is not yet available on PyPI, but the module can be pip installed locally. The directory should first be downloaded to your local machine, and can then be installed using the command:

pip install -e .

We also recommend you to install the EpiABM model and EpiOS to generate the data of infection simulation and do sampling.

For other CPU:

For Apple Silicon users, you should firstly use conda to install pystan. After this, you should manually uninstall the following packages: httpstan and pysimdjson. Next, you should go to the github repository of httpstan to download the 4.10.1 version and install it according to the documentation of httpstan for non-x86 CPU. Finally, use pip to install pysimdjson==5.0.2. Now you will have the correct pystan working on your Apple Silicon machine.

Documentation

Documentations can be accessed via the above docs badge.

Example Usage

Model description, examples and work summary can be found in the file work_summary.ipynb, with codes to use EpiPI to predict $R_t$. There are also definitions, description and reference for data used in this model.