yulab-smu/ncov2019

:microbe: Exploring COVID-19 data

nCov2019: An R package for exploring COVID-19 statistics

The package was developed since Jan. 2020 and originally hosted on GuangchuangYu/nCov2019. This repo contains an up-to-date version with data from new sources (from worldometers and JHUCSSE) and new data types (vaccine and therapeutics data).

🏠 Data Sources

• Latest data of coronavirus cases: worldometers
• Historical data of coronavirus cases : JHUCSSE
• Vaccine data: raps.org
• Therapeutics data: raps.org

Fetching data using API provided by disease.sh

Find out more on the vignette vignette.

✍️ Authors

Guangchuang YU and Tianzhi Wu

https://yulab-smu.top

If you use nCov2019, please cite the following article:

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("YuLab-SMU/nCov2019")

🔰 Usages

• res <- query() to query 5 types of statistics
  • global summary,
  • latest data
  • historical data
  • vaccine data
  • therapeutic data
• x <- res$global to access global summary data
  • summary(x) will return global overview
  • x$affectedCountries will return total affected countries,(other 20 types of statistics is available)
• y <- res$latest or y <- res$historical to access latest or historical data
  • y["global"] will return all countries' statistics
  • y[country] will return country level statistics
  • For countries in China, UK, Australia, Canada ,Denmark , France and Netherlands, provincial data is also available and y[country,province] will return statistics data of the selected province
• z <- res$vaccine or y <- res$therapeutics to access vaccine or therapeutic data
  • summary(z) will return the summary of their trial phase
  • z["all"] will return all candidate
  • z[ID="id1"] each vaccine or therapeutics candidate has an id, this will return detail description of the selected candidate (e.g., "id1")
• 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

• online vignette
• An R Package to Explore the Novel Coronavirus

📈 Shiny Apps that use nCov2019

• Coronavirus Tracking dashboard
• Novel Coronavirus Pneumonia (NCP-2019) Dashboard
• Coronavirus COVID-19 outbreak statistics and forecast

💖 Collected in resource list

• Open-Source-COVID-19
• Top 7 R resources on COVID-19 Coronavirus
• COVID-19 Coronavirus Disease resources

ncov2019's Issues

Using query() function

When using query() function, an error occurs at Querying historical data ...

the error is as follows. " Error in loadNamespace(name) : there is no package called ‘reshape2’"

Hence can now load res.

please advice,
Thank you