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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
message=FALSE,
warning=FALSE
)
```
# coronavirus <a href='https://RamiKrispin.github.io/coronavirus/'><img src='man/figures/coronavirus.png' align="right" /></a>
<!-- badges: start --->
[](https://github.com/RamiKrispin/coronavirus/actions?query=workflow%3Abuild)
[](https://cran.r-project.org/package=coronavirus)
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://opensource.org/licenses/MIT)
[](https://github.com/RamiKrispin/coronavirus/commit/master)
[](https://cran.r-project.org/package=coronavirus)
<!-- badges: end -->
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](https://github.com/CSSEGISandData/COVID-19).
More details available [here](https://RamiKrispin.github.io/coronavirus/), and a `csv` format of the package dataset available [here](https://github.com/RamiKrispin/coronavirus-csv)
A summary dashboard is available [here](https://ramikrispin.github.io/coronavirus_dashboard/)
<img src="man/figures/2019-nCoV-CDC-23312_without_background.png" width="65%" align="center"/></a>
<figcaption>Source: Centers for Disease Control and Prevention's Public Health Image Library </figcaption>
## 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:
```r
install.packages("coronavirus")
```
Install the Github version (refreshed on a daily bases):
``` r
# install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")
```
## Data refresh
While the **coronavirus** [CRAN version](https://cran.r-project.org/package=coronavirus) is updated every month or two, the [Github (Dev) version](https://github.com/RamiKrispin/coronavirus) is updated on a daily bases. The `update_dataset` function enables to overcome this gap and keep the installed version with the most recent data available on the Github version:
``` r
library(coronavirus)
update_dataset()
```
**Note:** must restart the R session to have the updates available
## Usage
```{r}
data("coronavirus")
```
This `coronavirus` dataset has the following fields:
```{r}
head(coronavirus)
tail(coronavirus)
```
Here is an example of a summary total cases by region and type (top 20):
```{r}
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)`):
```{r}
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/ <br>
* DXY.cn. Pneumonia. 2020. http://3g.dxy.cn/newh5/view/pneumonia. <br>
* BNO News: https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/ <br>
* 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 <br>
* Hong Kong Department of Health: https://www.chp.gov.hk/en/features/102465.html <br>
* Macau Government: https://www.ssm.gov.mo/portal/ <br>
* Taiwan CDC: https://sites.google.com/cdc.gov.tw/2019ncov/taiwan?authuser=0 <br>
* US CDC: https://www.cdc.gov/coronavirus/2019-ncov/index.html <br>
* Government of Canada: https://www.canada.ca/en/public-health/services/diseases/coronavirus.html <br>
* Australia Government Department of Health: https://www.health.gov.au/news/coronavirus-update-at-a-glance <br>
* European Centre for Disease Prevention and Control (ECDC): https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases <br>
<br>