covsirphy 2.8.0

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

CovsirPhy introduction

Documentation | Installation/Dataset preparation | Quickest usage | API reference

CovsirPhy is a Python package for COVID-19 (Coronavirus disease 2019) data analysis with phase-dependent SIR-derived ODE models. We can download datasets and analyse it easily. This will be a helpful tool for data-informed decision making. Please refer to “Method” part of Kaggle Notebook: COVID-19 data with SIR model to understand the methods.

Functionalities

• Data preparation and data visualization

• Phase setting with S-R Trend analysis

• Numerical simulation of ODE models

  • Stable: SIR, SIR-D and SIR-F model

  • Development: SIR-FV and SEWIR-F model

• Phase-dependent parameter estimation of ODE models

• Scenario analysis: Simulate the number of cases with user-defined parameter values

• (In development): Find the relationship of government response and parameter values

Inspiration

• Monitor the spread of COVID-19

• Keep track parameter values/reproduction number in each country/province

• Find the relationship of reproductive number and measures taken by each country

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.

Stable versions of Covsirphy are available at PyPI (The Python Package Index): covsirphy and support Python 3.7 or newer versions.

pip install covsirphy --upgrade

Development versions are in GitHub repository: CovsirPhy.

!pip install "git+https://github.com/lisphilar/covid19-sir.git#egg=covsirphy"

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

Guidotti, E., Ardia, D., (2020), “COVID-19 Data Hub”, Journal of Open Source Software 5(51):2376, doi: 10.21105/joss.02376.

Usage

Please read the following documents.

• Quickest version

• Quick version

• Details: phases

• Details: theoretical datasets

• Details: policy measures

• 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/