https://github.com/bnb32/corona_modeling

Compartmental epidemiology models for COVID
https://github.com/bnb32/corona_modeling

compartmental-models covid-19

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Compartmental epidemiology models for COVID

• Host: GitHub
• URL: https://github.com/bnb32/corona_modeling
• Owner: bnb32
• License: mit
• Created: 2021-08-17T04:08:16.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-06-01T17:48:17.000Z (over 2 years ago)
• Last Synced: 2024-10-14T03:07:03.872Z (3 months ago)
• Topics: compartmental-models, covid-19
• Language: Python
• Homepage:
• Size: 2.78 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
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COVID Modeling Overview

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Documentation

=============

``_

Installation

============

Follow instructions `here `_

Usage

=====

Instantiate model:

.. code-block:: python

    from covid.models import SIR

    model = SIR()

Instantiate dataset:

.. code-block:: python

    from covid.fetch import Dataset

    ds = Dataset({'state': , 'n_days': })

Get data:

.. code-block:: python

    data = ds.get_data()

Fit model parameters:

.. code-block:: python

    model.fit_parameters_from_data(data)

Run model:

.. code-block:: python

    model.initialize({k: data[k][0] for k in model.compartment_names})

    output = model.run_model(n_days=)

Plot output of specific compartment:

.. code-block:: python

    from covid.postprocessing import plot_compartment

    plot_compartment(sim_data=output, raw_data=data, params=ds.params, compartment=)

Change model parameters:

.. code-block:: python

    model.update_parameters()