In javierluraschi/covid: Dataset Generator for WHO COVID-19

This repo provides hourly updates from the World Helath Organization Coronavirus disease (COVID-2019) situation reports in CSV and pins format.

From R, you can query the list of available datasets as follows:

library(pins)

board_register_datatxt("https://raw.githubusercontent.com/javierluraschi/covid/datasets/data.txt", "covid")

pin_find(board = "covid")

You can then retrieve specific tables from the daily reports as follows:

pin_get("covid-20200227-1", board = "covid")

Do notice that this dataset come straight from the PDF files, while the data is kept up-to-date by parsing it as soon as it's released, the headers still need to be cleaned up and some tables joined together.

The CSV files can be found under covid/tree/datasets, a cleaned up dataset can be found in other repos like ramikrispin/coronavirus-csv and downloaded with pins as follows:

covid <- pin("https://raw.githubusercontent.com/RamiKrispin/coronavirus-csv/master/coronavirus_dataset.csv") %>%
  read.csv() %>% tibble::as_tibble() %>% print()

library(dplyr, warn.conflicts = FALSE)
library(ggplot2)

filter(covid, type == "confirmed") %>%
  group_by(date) %>%
  summarise(confirmed = sum(cases)) %>%
  arrange(date) %>%
  mutate(date = as.Date(date), confirmed = cumsum(confirmed)) %>%
  ggplot(aes(x=date, y=confirmed)) + geom_line() + theme_light()