In dmglandon/coronavirus_test: 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

Installation

Install the CRAN version:

install.packages("coronavirus") 

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

# install.packages("devtools")
devtools::install_github("RamiKrispin/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
  

dmglandon/coronavirus_test documentation built on March 23, 2020, 12:44 a.m.