A tool for downloading Spanish COVID-19 and mobility data
Project description
flowmaps-data
A tool for downloading COVID-19 and mobility datasets for Spain.
The database integrates two main types of data:
-
Time dependent population mobility networks across Spain (provided by MITMA and INE)
-
Daily reports of COVID-19 cases in Spain, at different levels of spatial resolution (provided by the CNE and the different Autonomous Communities)
All the data records are associated with a specific area from a geographic layer:
- Geographic layers for Spain, in geojson format, at different levels of spatial resolution.
All the data has been gather from official access points.
More info about the data: https://flowmaps.life.bsc.es/flowboard/data
API: https://flowmaps.life.bsc.es/api
Contact us: https://flowmaps.life.bsc.es/flowboard/contact
Installation
Install using pip:
pip install flowmaps-data
Install manually:
Create virtual environment:
virtualenv env --python=python3
source env/bin/activate
Install python dependencies:
pip3 install -r requirements.txt
Usage
Command line utility
usage: flowmaps-data [-h] COLLECTION [list describe download]
examples:
# Geojson layers
flowmaps-data layers list
flowmaps-data layers describe --layer cnig_provincias --provenance
flowmaps-data layers describe --layer cnig_provincias --plot
flowmaps-data layers download --layer cnig_provincias
# Consolidated COVID-19 data
flowmaps-data covid19 list
flowmaps-data covid19 describe --ev ES.covid_cpro
flowmaps-data covid19 download --ev ES.covid_cpro --output-file out.csv --output-type csv
# Population
flowmaps-data population list
flowmaps-data population describe --layer cnig_provincias
flowmaps-data population download --layer zbs_15 --output-file out.csv
# Origin-destination daily mobility (from MITMA)
flowmaps-data daily_mobility_matrix list
flowmaps-data daily_mobility_matrix describe
flowmaps-data daily_mobility_matrix download --source-layer cnig_provincias --target-layer cnig_provincias --start-date 2020-10-10 --end-date 2020-10-16 --output-file out.csv
# Daily zone movements (from MITMA)
flowmaps-data zone_movements list
flowmaps-data zone_movements describe
flowmaps-data zone_movements download --layer cnig_provincias --output-file out.csv --start-date 2020-10-10 --end-date 2020-10-10
# Raw datasets
flowmaps-data datasets list
flowmaps-data datasets describe --ev ES.covid_cpro
flowmaps-data datasets download --ev ES.covid_cpro --output-file out.csv --output-type csv
# Mobility Associated Risk
flowmaps-data risk list
flowmaps-data risk list-dates
flowmaps-data risk download --source-layer cnig_provincias --target-layer cnig_provincias --ev ES.covid_cpro --date 2020-10-10 --output-file out.csv --output-format csv
Python module
from flowmaps_data import geolayer, covid19, dataset, daily_mobility_matrix, population, zone_movements
# Geojson layers
geojson = geolayer('cnig_provincias')
# Consolidated COVID-19 data
df = covid19(ev='ES.covid_cpro')
# Raw health datasets
df = dataset(ev='ES.covid_cpro')
# Origin-destination daily mobility (from MITMA)
df = daily_mobility_matrix(source_layer='cnig_provincias', target_layer='cnig_provincias', start_date='2020-11-01', end_date='2020-12-01', source='28', target='08')
# Daily zone movements (from MITMA)
df = zone_movements(layer='cnig_provincias')
# Population
df = population('cnig_provincias')
More examples
Plot daily incidence by province
from flowmaps_data import geolayer, covid19
import plotly.graph_objects as go
# Download geojson layer
geojson = geolayer('cnig_provincias')
# Download COVID-19 data
df = covid19(ev='ES.covid_cpro')
# Select data for one date
date = '2020-10-10'
df = df[df['date'] == date]
# Plot
fig = go.Figure(go.Choroplethmapbox(geojson=geojson,
locations=date_df['id'],
z=date_df['new_cases'],
colorscale="Reds",
marker_opacity=0.8))
fig.update_layout(title=f'Covid-19 daily incidence at {date}',
mapbox_style="carto-positron",
mapbox_zoom=4.5,
mapbox_center={"lat": 40.495178477814555, "lon": -3.717336960173357})
fig.update_layout(margin={"r":0,"t":30,"l":0,"b":0})
fig.show()
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