[Docs] how to analyze Monkeypox 2022 linelist data with SIR-derived models

[lisphilar]

What dataset you need?

Confirmed/Fatal/Recovered data of Monkeypox 2022 on date for locations (ISO3, City etc.)

How will you use the dataset for your analysis?

With SIR-F model as the same way as COVID-19 data.

(Optional) Example datasets

https://github.com/globaldothealth/monkeypox

Linelist data should be converted with covsirphy internally.

[lisphilar]

I developed how to calculate the number of cases with the linelist data. https://www.kaggle.com/code/lisphilar/monkeypox-with-sir-derived-model

CovsirPhy provides a tool to get population data from COVID-19 Data Hub.

It may be better to demonstrate the way of calculation in documentation.

[lisphilar]

https://github.com/globaldothealth/monkeypox/issues/127

[lisphilar]

Notebooks should be revised because of something wrong with total calculation.

Use .set_index().combine_first().ffill().fillna(0).reindex().cumsum() rather than .merge().pivot_table()?

[lisphilar]

Revised: https://gist.github.com/lisphilar/ae24c369d21cfeb89a673de1f6edb2b9

[lisphilar]

With #1180 (pull request: #1213), population data is available:

import covsirphy as cs
dl = cs.DataDownloader()
dl.layer(databases=["wpp"])
dl.citations()

import covsirphy as cs
eng = cs.DataEngineer()
eng.download(databases=["wpp"])
eng.all()
eng.citations()