COVID-19 Data Hub
COVID-19 Data Hub - Published in JOSS (2020)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 13 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: scholar.google -
✓Committers with academic emails
1 of 22 committers (4.5%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution
Basic Info
- Host: GitHub
- Owner: covid19datahub
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://covid19datahub.io
- Size: 160 MB
Statistics
- Stars: 252
- Watchers: 12
- Forks: 92
- Open Issues: 2
- Releases: 1
Topics
Metadata Files
README.md
COVID-19 Data Hub 
Funded by the Institute for Data Valorization IVADO in 2020. Supported by the R Consortium from 2021 to 2024. Funded by the University of Lugano USI in 2025.
This repository aggregates COVID-19 data at a fine-grained spatial resolution from several sources and makes them available in the form of ready-to-use CSV files available at https://covid19datahub.io
| Variable | Description |
| ------------------------- | ------------------------------------------------------------ |
| confirmed | Cumulative number of confirmed cases |
| deaths | Cumulative number of deaths |
| recovered | Cumulative number of patients released from hospitals or reported recovered |
| tests | Cumulative number of tests |
| vaccines | Cumulative number of total doses administered |
| people_vaccinated | Cumulative number of people who received at least one vaccine dose |
| people_fully_vaccinated | Cumulative number of people who received all doses prescribed by the vaccination protocol |
| hosp | Number of hospitalized patients on date |
| icu | Number of hospitalized patients in intensive therapy on date |
| vent | Number of patients requiring invasive ventilation on date |
| population | Total population |
The dataset also includes policy measures by Oxford's government response tracker, and a set of keys to match the data with Google and Apple mobility reports, with the Hydromet dataset, and with spatial databases such as Eurostat for Europe or GADM worldwide.
Administrative divisions
The data are provided at 3 different levels of granularity:
- level 1: national-level data (e.g., countries)
- level 2: sub-national data (e.g., regions/states)
- level 3: lower-level data (e.g., municipalities/counties)
Download the data
All the data are available to download at the download centre.
How it works
COVID-19 Data Hub is developed around 2 concepts:
- data sources
- countries
To extract the data for one country, different data sources may be required. For this reason, the code in the R folder is organized in two main types of files:
- files representing a data source (prefix
ds_) - files representing a country (prefix
iso_)
The ds_ files implement a wrapper to pull the data from a provider and import them in an R data.frame with standardized column names. The iso_ files take care of merging all the data sources needed for one country, and to map the identifiers used by the provider to the id listed in the CSV files. Finally, the function covid19 takes care of downloading the data for all countries at all levels.
The code is run continuously on a dedicated Linux server to crunch the data from the providers. In principle, one can use the function covid19 from the repository to generate the same data we provide at the download centre. However, this takes between 1-2 hours, so that downloading the pre-computed files is typically more convenient.
Contribute
If you find some issues with the data, please report a bug.
Academic publications
The first version of the project is described in "COVID-19 Data Hub", Journal of Open Source Software, 2020. The implementation details and the latest version of the data are described in "A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution", Scientific Data, Nature, 2022. You can browse the publications that use COVID-19 Data Hub here and here. Please cite our paper(s) when using COVID-19 Data Hub.
Cite as
We have invested a lot of time and effort in creating COVID-19 Data Hub, please cite the following when using it:
Guidotti, E., Ardia, D., (2020), "COVID-19 Data Hub", Journal of Open Source Software 5(51):2376, doi: 10.21105/joss.02376.
A BibTeX entry for LaTeX users is:
latex
@Article{guidotti2020,
title = {COVID-19 Data Hub},
year = {2020},
doi = {10.21105/joss.02376},
author = {Emanuele Guidotti and David Ardia},
journal = {Journal of Open Source Software},
volume = {5},
number = {51},
pages = {2376}
}
The implementation details and the latest version of the data are described in:
Guidotti, E., (2022), "A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution", Sci Data 9, 112, doi: 10.1038/s41597-022-01245-1
A BibTeX entry for LaTeX users is:
latex
@Article{guidotti2022,
title = {A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution},
year = {2022},
doi = {10.1038/s41597-022-01245-1},
author = {Emanuele Guidotti},
journal = {Scientific Data},
volume = {9},
number = {1},
pages = {112}
}
Terms of use
By using COVID-19 Data Hub, you agree to our terms of use.
Supported by
Owner
- Name: COVID-19 Data Hub
- Login: covid19datahub
- Kind: organization
- Location: Worldwide
- Website: https://covid19datahub.io
- Repositories: 3
- Profile: https://github.com/covid19datahub
Unified dataset for a better understanding of COVID-19.
JOSS Publication
COVID-19 Data Hub
Authors
University of Neuchâtel, Switzerland
HEC Montréal, Canada
Editor
Will Rowe
Tags
COVID-19GitHub Events
Total
- Watch event: 2
- Push event: 352
- Pull request review comment event: 2
- Pull request review event: 3
- Pull request event: 3
- Fork event: 1
Last Year
- Watch event: 2
- Push event: 355
- Pull request review comment event: 2
- Pull request review event: 3
- Pull request event: 3
- Fork event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| emanuele-guidotti | e****i@h****t | 826 |
| Emanuele Guidotti | e****i@u****h | 118 |
| Martin Beneš | m****6@g****m | 46 |
| sim55649 | s****9@g****m | 24 |
| David Ardia | A****D | 21 |
| ViktoriiaTan | v****a@g****m | 11 |
| Elsa Burren | 6****n | 10 |
| FedericoLG | l****e@g****m | 7 |
| rijinbaby | r****6@g****m | 6 |
| Dan Kelley | k****n@g****m | 4 |
| Estella | e****9@g****m | 4 |
| muhammedseehan-commits | 6****s | 4 |
| Angelina Khatiwada | 6****a | 3 |
| montemurroPaolo | 4****o | 3 |
| Matt Bolton | z****a@g****m | 2 |
| Robert Rosca | 3****a | 2 |
| guilhermegfv | 7****v | 2 |
| jonekeat | j****t@g****m | 2 |
| yuan zhou | s****n@g****m | 2 |
| Will Rowe | w****e@b****k | 1 |
| PaoloMontemurro | m****p@u****h | 1 |
| Xiangyun Huang | x****h@o****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 88
- Total pull requests: 21
- Average time to close issues: 24 days
- Average time to close pull requests: 16 days
- Total issue authors: 47
- Total pull request authors: 11
- Average comments per issue: 4.48
- Average comments per pull request: 1.67
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 6
- Average time to close issues: N/A
- Average time to close pull requests: 9 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kenshermock (16)
- utterances-bot (8)
- hlcny (8)
- guenterhack (5)
- umbe1987 (3)
- vzemlys (2)
- AlFontal (2)
- felipemfp (2)
- susanapsilva (2)
- Marina-Antillon (2)
- eguidotti (2)
- LuiNov (1)
- terrytsaistats (1)
- PowershellNinja (1)
- pmaier1971 (1)
Pull Request Authors
- ViktoriiaTan (6)
- estellad (4)
- martinbenes1996 (3)
- hanzlan (1)
- anant-procogia (1)
- ftrotter (1)
- esuess (1)
- guilhermegfv (1)
- sim55649 (1)
- vzemlys (1)
- jonekeat (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
- Total downloads: unknown
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 6
proxy.golang.org: github.com/covid19datahub/COVID19
- Documentation: https://pkg.go.dev/github.com/covid19datahub/COVID19#section-documentation
- License: gpl-3.0
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Latest release: v3.0.0+incompatible
published over 4 years ago
Rankings
proxy.golang.org: github.com/covid19datahub/covid19
- Documentation: https://pkg.go.dev/github.com/covid19datahub/covid19#section-documentation
- License: gpl-3.0
-
Latest release: v3.0.0+incompatible
published over 4 years ago
Rankings
Dependencies
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite
- R >= 3.5.0 depends
- dplyr >= 1.0.0 depends
- tidyr >= 1.0.0 depends
- utils * depends
- MMWRweek * imports
- R.utils * imports
- curl * imports
- data.table * imports
- digest * imports
- httr * imports
- jsonlite * imports
- readr * imports
- readxl * imports
- remotes * imports
- rvest * imports
- xml2 * imports
- knitr * suggests
- rmarkdown * suggests