Covid-Health

A Buildnn open source project.

Huge transcoding effort to standardize national and international datasets about COVID-19.

Installation

$ pip install git+https://github.com/ggbaro/covid-health-ita.git

Basic Usage

Build locally your own data sets for Coronavirus situational awareness using the command line tool covid-data.

$ covid-data
Usage: covid-data [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  eurostat
  ita
  worldometers  choose figure between ['age_sex_demographics', 'countries']

Every data source has its own sub-command

$ covid-data eurostat --help
Usage: covid-data eurostat [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  from-eurostat  one of ['demo_r_d2jan', 'demo_r_pjangrp3',
                 'demo_r_d3dens',...

  list-datasets  List available datasets

For Eurostat and other sources, there are help functions such as list-datasets:

$ covid-data eurostat list-datasets
[0] demo_r_d2jan -> Population on 1 January by age, sex and NUTS 2 region
[1] demo_r_pjangrp3 -> Population on 1 January by age group, sex and NUTS 3 region
...
[5] hlth_sha11_hf -> Health care expenditure by financing scheme
[69] hlth_ehis_hc6 -> Self-reported consultation of a psychologist or physiotherapist by sex, age and educational attainment level (%)

You can build your datset locally in no time:

$ covid-data eurostat from-eurostat --ext .csv.gz demo_r_d2jan
saving to:  ./data/interim/eurostat/demo_r_d2jan.csv.gz
         NUTS    unit  gender     age  year population
0          AL  number  female   TOTAL  2010   1459025 
1         AL0  number  female   TOTAL  2010   1459025 
2        AL01  number  female   TOTAL  2010           
3        AL02  number  female   TOTAL  2010           
4        AL03  number  female   TOTAL  2010           
...       ...     ...     ...     ...   ...        ...
5090845  UKM7  number   total  Y_OPEN  2016       342 
5090846  UKM8  number   total  Y_OPEN  2016       231 
5090847  UKM9  number   total  Y_OPEN  2016       164 
5090848   UKN  number   total  Y_OPEN  2016       274 
5090849  UKN0  number   total  Y_OPEN  2016       274 

[5090850 rows x 6 columns]

Data Sources

World

Category	Name	Type	URL	cli
Unofficial Web Source	Worldometer	Covid19	worldometers.info	`$ covid-data worldometers`

Europe

Category	Name	Type	URL	cli
Institutional DB	Eurostat	Open Data	ec.europa.eu/eurostat	`$ covid-data eurostat`

Italy

Submodule covid_health.ita

Category	Name	Type	URL	cli
Insititutional DB	Istat	Open Data	dati.istat.it	`$ covid-data ita istat`
Institutional DB	Open Data della Pubblica Amministrazione Italiana - AGID	Health Open Data	dati.gov.it	`$ covid-data ita salute-gov`
Official Git Repo	Protezione Civile - COVID-19	COVID-19 Data	github.com/pcm-dpc/COVID-19	`$`
Unofficial Git Repo	Covid19italia	COVID-19 Data	github.com/ondata/covid19italia	`$`

Dimensions

Project Organization

.
├── data
│   ├── external
│   ├── interim
│   ├── processed
│   └── raw
├── LICENSE
├── MANIFEST.in
├── notebooks
├── README.md
├── requirements-dev.txt
├── requirements.txt
├── setup.py
└── src
    └── covid_health
        ├── cli.py
        ├── __init_.py
        ├── ita
        ├── prep_eurostat.py
        ├── prep_worldometer.py
        ├── retrieve_eurostat.py
        ├── transcoding
        └── utils.py