/nCov2019

query stats of infected coronavirus cases

Primary LanguageR

nCov2019: An R package with real-time data, historical data and Shiny app

Please visit https://github.com/YuLab-SMU/nCov2019 for an up-to-date version.

This package is one of the earliest R packages that designed to query COVID data. It is available since Jan. 2020, at the time there were few data resources available (see our blog post (in Chinese) (Feb. 03, 2020) and another blog post by third party (in English) (Feb. 11, 2020)).

🏠 Data Sources

Real-time data

Historical data (three public data sources):

  1. Wuhan-2019-nCoV GitHub repository.

    • This data source contains detailed city level data in China, and country level data in worldwide.

  2. National Health Commission of the People’s Republic of China

    • This data source contains province level data in China.

  3. DXY.cn. Pneumonia. 2020.

    • We collect historical city level data in China from this source.

  4. 今日头条

    • We collect historical province level data for oversea countries form this source. (Start from 2020-03-15)

      The user can obtain the historical provincial data in China, South Korea, United States, Japan, Iran, Italy, Germany and United Kingdom now.

      For example, the below will return the historical data for Italy.

      library(nCov2019)
nCov2019_set_country(country = 'Italy') 
x['province'] # this will return Italy data only.

For more details see our vignette, Preprint, and Shiny app.

✍️ Authors

If you use nCov2019, please cite the following paper:

Wu T, Hu E, Ge X*, Yu G*. 2021. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ 9:e11421 https://doi.org/10.7717/peerj.11421

⏬ Installation

Get the development version from github:

## install.packages("remotes")
remotes::install_github("GuangchuangYu/nCov2019")
  • get_nCov2019() to query online latest information
  • load_nCov2019() to get historical data
  • nCov2019_set_country() to set country options
  • summary and [ to access data
  • plot to present data on map
  • dashboard() to open Shiny app dashboard

🎨 Example

Run the script example.R in R using source("example.R"), will produce the following figure:

📖 Documents

📈 Shiny Apps that use nCov2019

💖 Collected in resource list