In adityasinhak/coronavirus: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

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coronavirus

The coronavirus package provides a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic. The raw data pulled from the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus repository.

More details available here, and a csv format of the package dataset available here

A summary dashboard is available here

Source: Centers for Disease Control and Prevention's Public Health Image Library

Important Note

As this an ongoing situation, frequent changes in the data format may occur, please visit the package news to get updates about those changes

Installation

Install the CRAN version:

install.packages("coronavirus")

Install the Github version (refreshed on a daily bases):

# install.packages("devtools")
devtools::install_github("covid19r/coronavirus")

Usage

The package contains a single dataset - coronavirus:

library(coronavirus) 

data("coronavirus")

This coronavirus dataset has the following fields:

head(coronavirus) 
tail(coronavirus) 

Here is an example of a summary total cases by region and type (top 20):

library(dplyr)

summary_df <- coronavirus %>% group_by(Country.Region, type) %>%
  summarise(total_cases = sum(cases)) %>%
  arrange(-total_cases)

summary_df %>% head(20) 

Summary of new cases during the past 24 hours by country and type (as of r max(coronavirus$date)):

library(tidyr)

coronavirus %>% 
  filter(date == max(date)) %>%
  select(country = Country.Region, type, cases) %>%
  group_by(country, type) %>%
  summarise(total_cases = sum(cases)) %>%
  pivot_wider(names_from = type,
              values_from = total_cases) %>%
  arrange(-confirmed)

Data Sources

The raw data pulled and arranged by the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) from the following resources:

• World Health Organization (WHO): https://www.who.int/
  
• DXY.cn. Pneumonia. 2020. http://3g.dxy.cn/newh5/view/pneumonia.
  
• BNO News: https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/
  
• National Health Commission of the People’s Republic of China (NHC): http:://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml
• China CDC (CCDC): http:://weekly.chinacdc.cn/news/TrackingtheEpidemic.htm
  
• Hong Kong Department of Health: https://www.chp.gov.hk/en/features/102465.html
  
• Macau Government: https://www.ssm.gov.mo/portal/
  
• Taiwan CDC: https://sites.google.com/cdc.gov.tw/2019ncov/taiwan?authuser=0
  
• US CDC: https://www.cdc.gov/coronavirus/2019-ncov/index.html
  
• Government of Canada: https://www.canada.ca/en/public-health/services/diseases/coronavirus.html
  
• Australia Government Department of Health: https://www.health.gov.au/news/coronavirus-update-at-a-glance
  
• European Centre for Disease Prevention and Control (ECDC): https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases
  

adityasinhak/coronavirus documentation built on April 21, 2020, 7:28 a.m.