Package for COVID-19 analysis with SIR-derived ODE models
Project description
CovsirPhy is a Python package for COVID-19 (Coronavirus disease 2019) data analysis with SIR-derived ODE models. Please refer to “Method” part of COVID-19 data with SIR model notebook in Kaggle to understand the methods.
Functionalities
Downloading and cleaning data: refer to “Installation and dataset preparation” section
Data visualization
S-R Trend analysis to determine the change points of parameters
Numerical simulation of ODE models
Description of ODE models
Basic class of ODE models
SIR, SIR-D, SIR-F, SIR-FV and SEWIR-F model
Parameter Estimation of ODE models
Scenario analysis: Simulate the number of cases with user-defined parameter values
Inspiration
Monitor the spread of COVID-19
Keep track parameter values/reproductive number in each country/province
Find the relationship of reproductive number and measures taken in each country/province
If you have ideas or need new functionalities, please join this project. Any suggestions with Github Issues are always welcomed. Please read Guideline of contribution in advance.
Installation and dataset preparation
We have the following options to start analysis with CovsirPhy. Datasets are not included in this package, but we can prepare them with DataLoader class.
Installation |
Dataset preparation |
|
---|---|---|
Standard users |
pip/pipenv |
Automated with DataLoader class |
Developers |
git-cloning |
Automated with DataLoader class |
Kagglers (local environment) |
git-cloning |
Kaggle API and Python script |
Kagglers (Kaggle platform) |
pip |
Kaggle Datasets |
Installation and dataset preparation explains how to install and prepare datasets for all users.
Covsirphy is available at PyPI (The Python Package Index): covsirphy and supports Python 3.7 or newer versions.
pip install covsirphy --upgrade
Usage
Please read the following documents.
License: Apache License 2.0
Please refer to LICENSE file.
Citation
CovsirPhy Development Team (2020), CovsirPhy, Python package for COVID-19 analysis with SIR-derived ODE models, https://github.com/lisphilar/covid19-sir
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