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
Install the CRAN version:
install.packages("coronavirus")Install the Github version (refreshed on a daily bases):
# install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")The package contains a single dataset - coronavirus:
library(coronavirus)
data("coronavirus")This coronavirus dataset has the following fields:
head(coronavirus)
#> Province.State Country.Region Lat Long date cases type
#> 1 Afghanistan 33 65 2020-01-22 0 confirmed
#> 2 Afghanistan 33 65 2020-01-23 0 confirmed
#> 3 Afghanistan 33 65 2020-01-24 0 confirmed
#> 4 Afghanistan 33 65 2020-01-25 0 confirmed
#> 5 Afghanistan 33 65 2020-01-26 0 confirmed
#> 6 Afghanistan 33 65 2020-01-27 0 confirmed
tail(coronavirus)
#> Province.State Country.Region Lat Long date cases type
#> 33043 Zhejiang China 29.1832 120.0934 2020-03-07 7 recovered
#> 33044 Zhejiang China 29.1832 120.0934 2020-03-08 7 recovered
#> 33045 Zhejiang China 29.1832 120.0934 2020-03-09 15 recovered
#> 33046 Zhejiang China 29.1832 120.0934 2020-03-10 15 recovered
#> 33047 Zhejiang China 29.1832 120.0934 2020-03-11 4 recovered
#> 33048 Zhejiang China 29.1832 120.0934 2020-03-12 2 recoveredHere 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)
#> # A tibble: 20 x 3
#> # Groups: Country.Region [15]
#> Country.Region type total_cases
#> <chr> <chr> <int>
#> 1 China confirmed 80932
#> 2 China recovered 62901
#> 3 Italy confirmed 12462
#> 4 Iran confirmed 10075
#> 5 Korea, South confirmed 7869
#> 6 China death 3172
#> 7 Iran recovered 2959
#> 8 France confirmed 2284
#> 9 Spain confirmed 2277
#> 10 Germany confirmed 2078
#> 11 US confirmed 1663
#> 12 Italy recovered 1045
#> 13 Italy death 827
#> 14 Norway confirmed 702
#> 15 Cruise Ship confirmed 696
#> 16 Switzerland confirmed 652
#> 17 Japan confirmed 639
#> 18 Denmark confirmed 617
#> 19 Sweden confirmed 599
#> 20 Netherlands confirmed 503Summary of new cases during the past 24 hours by country and type (as of 2020-03-12):
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)
#> # A tibble: 116 x 4
#> # Groups: country [116]
#> country confirmed death recovered
#> <chr> <int> <int> <int>
#> 1 Iran 1075 75 0
#> 2 US 382 4 4
#> 3 Denmark 173 0 0
#> 4 Germany 170 0 0
#> 5 Korea, South 114 6 45
#> 6 Norway 104 0 0
#> 7 Sweden 99 0 0
#> 8 Austria 56 1 0
#> 9 Slovenia 32 0 0
#> 10 Saudi Arabia 24 0 0
#> 11 Israel 22 0 0
#> 12 Iceland 18 0 0
#> 13 Poland 18 1 0
#> 14 Brazil 14 0 0
#> 15 Luxembourg 12 0 0
#> 16 Albania 11 0 0
#> 17 China 11 11 1257
#> 18 India 11 0 0
#> 19 Thailand 11 0 0
#> 20 United Arab Emirates 11 0 0
#> 21 Canada 9 0 0
#> 22 Costa Rica 9 0 0
#> 23 Kuwait 8 0 3
#> 24 Russia 8 0 0
#> 25 Egypt 7 0 0
#> 26 San Marino 7 1 0
#> 27 Serbia 7 0 0
#> 28 Slovakia 6 0 0
#> 29 Algeria 4 1 8
#> 30 Bosnia and Herzegovina 4 0 0
#> 31 Mexico 4 0 0
#> 32 Peru 4 0 0
#> 33 Romania 4 0 0
#> 34 South Africa 4 0 0
#> 35 Armenia 3 0 0
#> 36 Belarus 3 0 0
#> 37 Cuba 3 0 0
#> 38 Czechia 3 0 0
#> 39 Panama 3 0 0
#> 40 Philippines 3 1 0
#> # … with 76 more rowsThe 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
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