Vaccontrib: Quantifying the contributions unvaccinated and vaccinated subpopulations make towards the infection dynamics

# 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/

```python
>>> 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](https://github.com/benmaier/vaccontrib/blob/main/cookbook/notebooks/covid_examples.ipynb) and an [explanatory notebook including stochastic simulations](https://github.com/benmaier/vaccontrib/blob/main/cookbook/notebooks/first_examples.ipynb).

## 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](https://medrxiv.org/cgi/content/short/2021.11.24.21266831v1). To replicate the results, use the scripts in the [paper\_analysis](https://github.com/benmaier/vaccontrib/tree/main/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](https://github.com/benmaier/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`.

## License

This project is licensed under the [MIT License](https://github.com/benmaier/vaccontrib/blob/main/LICENSE).
Note that this excludes any images/pictures/figures shown here or in the documentation.