COVID19 - Coronavirus case data (country summary data)

Question

There are some very good sites showing the state of infections 'now', but I would like to find a data set of COVID-19 infections, deaths and number of tests by day and by country. These are the best I can find, but it doesn't quite meet what I'm after.

Notes:

There is another question about clinical data for covid19.
There is a community wiki answer to index the answers. You can answer there by editing, either adding a link to your answer, or a link to a "link-only" answer.

https://nextstrain.org/ncov points to gisaid.org as their data source. — TemporalWolf, Mar 05 '20 at 19:54
@TemporalWolf - Nextstrain powers the GISAID graphics but the date comes from the Johns Hopkins CSSE: see the running title in the black graphic here: https://www.gisaid.org/epiflu-applications/global-cases-covid-19/ — bob1, Mar 05 '20 at 22:58
this question's answers are a pie in the sky, dream come true for me. practically all are versioned databases. great job everyone! — albert, Apr 06 '20 at 19:24

philshem · Answer 1 · 2020-03-26T19:56:41.863

The JHU dashboard you linked has their data available as CSV on Github:

https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data

in particular these CSV files, which contain all historical timeseries

https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

Here is a coincidental Python3 scraper for the "confirmed cases", which reads the online CSV and does some parsing.

https://gist.github.com/philshem/fb60c1697f46f66b184c1f624283fd6a

#!/usr/bin/python3

# pip3 install pandas matplotlib
import pandas as pd
from matplotlib import pyplot as plt

# this gets the worldwide confirmed cases from JHU
url = 'https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv'

# read/download csv
df = pd.read_csv(url)

# filter on Swiss data
# df = df[df['Country/Region'] == 'Switzerland']

# remove unneeded columns
df.drop(['Province/State', 'Lat','Long'], axis=1, inplace=True)

# unpivot aka "melt"
df = df.melt(id_vars=['Country/Region'], var_name='date', value_name='confirmed_cases')

# rename column
df.rename(columns={'Country/Region': 'country'}, inplace=True)

# convert date column to date-type
df.date = pd.to_datetime(df.date)

# not needed
#df = df.set_index(df.date)

df.to_csv('confirmed_coronavirus.csv',index=False)
#print(df)

# write to plot, save as file
plt.plot(df.date, df.confirmed_cases, '-')
_ = plt.xticks(rotation=45)
plt.savefig('confirmed_coronavirus.png')

There is also an API source for the JHU data:

https://covid19api.com/#details

Access data on COVID19 through an easy API for free. Build dashboards, mobile apps or integrate in to other applications. Data is sourced from Johns Hopkins CSSE

Documentation: https://documenter.getpostman.com/view/10808728/SzS8rjbc

This dataset seems stopped updating as of March 22, 2020. Any ideas of an alternative? — David Nehme, Mar 25 '20 at 20:45
@DavidNehme seems just a lag to update the files. See yesterday e.g. https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_daily_reports/03-25-2020.csv — philshem, Mar 26 '20 at 19:28

score 11 · Accepted Answer · edited May 22 '20 at 18:38

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Index of Countries (community wiki)

Global

Europe

Belgium
Germany and another Germany
Switzerland
Spain
Italy
United Kingdom
- United Kingdom Overall
- Country, Region and Local Authority

North America

United States
- NY Times county level
- CDC

Asia

Oceania

edited May 22 '20 at 18:38

Marcus D

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answered Mar 31 '20 at 15:31

philshem

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For Germany, I'd like to point to https://github.com/jgehrcke/covid-19-germany-gae -- official time series data for individual counties / states. Proper CSV files for robust parsing. Updated daily. With improving history as historical data gets better over time. – Dr. Jan-Philip Gehrcke Dec 27 '20 at 16:15

score 9 · Answer 3 · answered Mar 18 '20 at 12:03

The Italian data from the Civil Protection Agency is updated daily at

https://github.com/pcm-dpc/COVID-19

There are a few data sets (CSV) in there. Aggregated data is published at http://opendatadpc.maps.arcgis.com/apps/opsdashboard/index.html#/b0c68bce2cce478eaac82fe38d4138b1

score 6 · Answer 4 · answered Mar 23 '20 at 09:52

6

I successfully parse WHO situation reports and convert them to CSV, from march 1. Older reports are too unstructured. See here: https://github.com/gibello/whocovid19 (reports in data/csv). On the site, also links to ECDC and Johns Hopkins data.

answered Mar 23 '20 at 09:52

Pierre-Yves Gibello

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score 6 · Answer 5 · answered Mar 23 '20 at 10:51

The CDC has US-wide cases, per date

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/testing-in-us.html

It's an HTML table, and I haven't found a more machine readable source. But with Python & Pandas you can easily read the data into a dataframe

import pandas as pd
df = pd.read_html('https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/testing-in-us.html')

print(df[0])

And to dump to a local CSV file, which will require some post-processing

df[0].to_csv('cdc.csv',index=False)

Date Collected,CDC Labs,US Public Health Labs
1/18,4,0
1/19,0,0
1/20,7,0
1/21,3,0
1/22,10,0
1/23,36,0
1/24,53,0
1/25,101,0
1/26,79,0
1/27,77,0
...

You'll need these packages

pip install pandas html5lib lxml

score 6 · Answer 6 · answered Mar 23 '20 at 14:42

6

German data can be found here:

https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Fallzahlen.html

answered Mar 23 '20 at 14:42

Parseltongue

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German data on the county level are linked here: https://opendata.stackexchange.com/a/17304/23668 – Peter Mar 29 '20 at 14:22

Peter · Answer 7 · 2020-11-12T14:05:21.573

German Covid-19 data from RKI (Robert Koch-Institut) on the state (Bundesländer) and county (Kreise) level can be found here.

Data on the county level include patient information such as age group and gender. County level data can be merged with county level information from the INKAR database via county id (Kreiskennziffer).

Update (2020-03-30): There is now a register of intensive care capacities in German hospitals.

Update (2020-04-06): An overview of the situation in Austria, can be found here. Find the official dashboard of the Ministry of Health (Gesundheitsministerium) here.

Update (2020-04-06): A timeseries of cases and deaths in Germany can be found here (updated every couple of days).

Update (2020-11-12): Find an overview of antibody studies in Germany here.

A plot and .csv of covid-19 cases and nr. hospitalized in Germany per week, 2 March to 23 August, are under https://gist.github.com/denis-bz/. Also jgehrcke/covid-19-germany-gae had .csv s with RKI data per day and city / Landkreis, updated twice a week or so. — denis, Aug 28 '20 at 15:36

philshem · Answer 8 · 2020-03-28T18:17:16.777

5

Several places for data of Switzerland Covid-19 cases

quasi-official: https://github.com/openZH/covid_19

~~unofficial: https://github.com/daenuprobst/covid19-cases-switzerland~~

Comparison between Swiss sources, including links to sources : https://observablehq.com/@republik/sars-cov-2-covid-19-data

more to come (hopefully data, not cases)

edited Mar 28 '20 at 18:17

answered Mar 18 '20 at 13:18

philshem

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For switzerland, a great source is: https://opendata.stackexchange.com/a/18498/18246 – Luke Skywalker Feb 09 '21 at 07:26

score 5 · Answer 9 · answered Mar 23 '20 at 14:46

5

Spain data can be found here:

https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/situacionActual.htm

answered Mar 23 '20 at 14:46

Parseltongue

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It's better if you merge your answers into one – Mar 23 '20 at 15:38

score 5 · Answer 10 · answered Mar 28 '20 at 12:34

My take on UK data: https://github.com/sainnr/covid19-uk-data-capture. The goal is to represent daily updates published by UK official bodies in the machine-readable format.

Currently, it consists mainly of two parts:

number of cases within the UK (fatal/recovered/positive/total) from 30 Jan till today
number of confirmed positive cases within regions (local authorities) breakdown

I'm a sole maintainer at the moment and do my best to update it within 24h after the publication of daily numbers.

Hope this helps someone to build anything useful on top!

score 4 · Answer 11 · answered Mar 31 '20 at 04:04

4

Chinese data: https://github.com/Avens666/COVID-19-2019-nCoV-Infection-Data-cleaning-

It is incomplete (from February to March 19th) and the explanations are in Chinese.

answered Mar 31 '20 at 04:04

Vicky Ding

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score 4 · Answer 12 · answered Apr 01 '20 at 07:26

ECDC (European centre for disease prevention & control) world data in CSV format, frequently updated: https://opendata.ecdc.europa.eu/covid19/casedistribution/csv

(From https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide - there's also xml and json)

score 3 · Answer 13 · answered Apr 02 '20 at 07:25

I have made a repository on github to crawl the data from wikipedia about southeast asia countries (Singapore, Malaysia, Vietnam, Thailand etc), as data for all other countries are widely collected.

https://github.com/caiyundong/covid19-sea

The approach of crawling can be used for other countries, and the data can be generated for API usage or file (json or csv).

score 3 · Answer 14 · answered Apr 22 '20 at 11:46

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Novel COVID 2019 Datasets by country, state in CSV format, frequently updated: WorldData.AI

answered Apr 22 '20 at 11:46

Catherine

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score 2 · Answer 15 · answered Apr 26 '20 at 16:51

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ESRI has their own Open Data

https://hub.arcgis.com/search

It has shapefiles that you take a look before download it

answered Apr 26 '20 at 16:51

PROBERT

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