Metadata-Version: 1.2
Name: vaccontrib
Version: 0.0.1
Summary: Quantifying the contributions vaccinated individuals make towards the effective reproduction number.
Home-page: https://github.com/benmaier/vaccontrib
Author: Benjamin F. Maier
Author-email: contact@benmaier.org
License: MIT
Project-URL: Documentation, http://vaccontrib.readthedocs.io
Project-URL: Contributing Statement, https://github.com/benmaier/vaccontrib/blob/master/CONTRIBUTING.md
Project-URL: Bug Reports, https://github.com/benmaier/vaccontrib/issues
Project-URL: Source, https://github.com/benmaier/vaccontrib/
Project-URL: PyPI, https://pypi.org/project/vaccontrib/
Description: 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/
        
        .. code:: 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
        -------
        
        .. code:: bash
        
           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
        ----------
        
        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
        
        .. code:: bash
        
           python compute.py DIRNAME1 DIRNAME2
        
        e.g.
        
        .. code:: bash
        
           python compute.py 00_lower 01_upper
        
        See the help text:
        
        .. code:: bash
        
           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.
        
        Changelog
        ---------
        
        Changes are logged in a `separate
        file <https://github.com/benmaier/vaccontrib/blob/main/CHANGELOG.md>`__.
        
        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.
        
        Contributing
        ------------
        
        If you want to contribute to this project, please make sure to read the
        `code of
        conduct <https://github.com/benmaier/vaccontrib/blob/main/CODE_OF_CONDUCT.md>`__
        and the `contributing
        guidelines <https://github.com/benmaier/vaccontrib/blob/main/CONTRIBUTING.md>`__.
        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 <https://github.com/benmaier/vaccontrib/blob/main/OUTLOOK.md>`__.
        
        |Contributor Covenant|
        
        Dev notes
        ---------
        
        Fork this repository, clone it, and install it in dev mode.
        
        .. code:: bash
        
           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``
        
        .. code:: bash
        
           make readme
        
        It will give you warnings about bad ``.rst``-syntax. Fix those errors in
        ``README.rst``. Then wrap the whole thing
        
        .. code:: bash
        
           make pypi
        
        It will probably give you more warnings about ``.rst``-syntax. Fix those
        until the warnings disappear. Then do
        
        .. code:: bash
        
           make upload
        
        .. |Contributor Covenant| image:: https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg
           :target: code-of-conduct.md
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
