vaccontrib

Code to quantify the contributions unvaccinated and vaccinated subpopulations make towards the effectie reproduction number and new infections.

repository: https://github.com/benmaier/vaccontrib/
documentation: http://vaccontrib.readthedocs.io/

>>> from vaccontrib.covid import get_reduced_vaccinated_susceptible_contribution_matrix_covid
>>> R0 = 6
>>> C = get_reduced_vaccinated_susceptible_contribution_matrix_covid(R0,variant='delta')
>>> C/C.sum()
array([[0.38159051, 0.17360365],
       [0.28493897, 0.15986686]])

Also, check out the tutorial notebook and an explanatory notebook including stochastic simulations.

Install

git clone git@github.com:benmaier/vaccontrib.git
pip install ./vaccontrib

vaccontrib was developed and tested for

Python 3.6
Python 3.7
Python 3.8

So far, the package's functionality was tested on Mac OS X and CentOS only.

Dependencies

vaccontrib directly depends on the following packages which will be installed by pip during the installation process

numpy>=1.17
matplotlib>=3.3
bfmplot>=0.0.11

Manuscript

Analysis and Results

Results found using this software package were reported in a preprint. To replicate the results, use the scripts in the paper_analysis directory. E.g. to get a comprehensive overview of results for a parameterset, run

python compute.py DIRNAME1 DIRNAME2

e.g.

python compute.py 00_lower 01_upper

See the help text:

usage: compute.py [-h] [-u RU] [-v RV] [-f] [-R R0] dirs [dirs ...]

Compute contribution matrices.

positional arguments:
  dirs                directories for which contributions matrices should be computed

optional arguments:
  -h, --help          show this help message and exit
  -u RU, --Ru RU      Base R-value of unvaccinated
  -v RV, --Rv RV      Base R-value of vaccinated
  -f, --save-figures  create, show, and save illustrations
  -R R0, --R0 R0      Base R0 to which the contribution will be scaled

Make sure you have numpyarray_to_latex installed.

Data in Figures

To comply with journal policies, all data shown in figures can be found in the file FigureData.xlsx.

Changelog

Changes are logged in a separate file.

License

This project is licensed under the MIT License. Note that this excludes any images/pictures/figures shown here or in the documentation.

Contributing

If you want to contribute to this project, please make sure to read the code of conduct and the contributing guidelines. In case you're wondering about what to contribute, we're always collecting ideas of what we want to implement next in the outlook notes.

Dev notes

Fork this repository, clone it, and install it in dev mode.

git clone git@github.com:YOURUSERNAME/vaccontrib.git
make

If you want to upload to PyPI, first convert the new README.md to README.rst

make readme

It will give you warnings about bad .rst-syntax. Fix those errors in README.rst. Then wrap the whole thing

make pypi

It will probably give you more warnings about .rst-syntax. Fix those until the warnings disappear. Then do

make upload