covsirphy 2.5.3

Package for COVID-19 analysis with SIR-derived ODE models

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

• 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

Main datasets will be retrieved via COVID-19 Data Hub and the citation is

Guidotti, E., Ardia, D., (2020), “COVID-19 Data Hub”, Working paper, doi: 10.13140/RG.2.2.11649.81763.

Usage

Please read the following documents.

• Usage (quickest version)

• Usage (quick version)

• Example codes in “example” directory of this repository

• Kaggle: COVID-19 data with SIR model

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

Related work

Method of analysis in CovsirPhy:

Lisphilar (2020), Kaggle notebook, COVID-19 data with SIR model, https://www.kaggle.com/lisphilar/covid-19-data-with-sir-model

Reproduction number evolution in each country:

Ilyass Tabiai and Houda Kaddioui (2020), GitHub pages, COVID19 R0 tracker, https://ilylabs.github.io/projects/COVID-trackers/