Created
February 13, 2020 17:27
-
-
Save johnburnmurdoch/bb2342ea81d3b1ce598084cfc626f390 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| install.packages("needs") | |
| library(needs) | |
| needs(tidyverse, magrittr, rvest, zoo, scales) | |
| WHO_sars_links <- read_html("https://www.who.int/csr/sars/country/en/") %>% | |
| html_nodes("ul.auto_archive") %>% | |
| magrittr::extract(1) %>% | |
| html_nodes("li a") %>% | |
| map_dfr(~{ | |
| link <- .x %>% html_attr("href") %>% paste0("https://www.who.int",.) | |
| date <- .x %>% html_text(T) %>% as.Date("%d %B %Y") | |
| tibble(date, link) | |
| }) | |
| WHO_sars_links %>% | |
| split(.$date) %>% | |
| imap_dfr(~{ | |
| message(.y) | |
| page <- read_html(.x$link) | |
| final_row <- page %>% html_nodes("div#primary table tr:nth-last-child(1)") | |
| final_row <- final_row %>% html_text(T) | |
| final_row <- final_row %>% keep(~ grepl("Total",.x)) | |
| total <- final_row %>% str_extract("\\d{3,4}") %>% parse_number() | |
| tibble(date = .x$date, total) | |
| }) -> WHO_sars_totals | |
| covid_totals <- read_html("https://www.worldometers.info/coronavirus/coronavirus-cases/") %>% | |
| html_nodes("body > div.container > div:nth-child(2) > div.col-md-8 > div > div:nth-child(17) > div:nth-child(2) > div > table tbody tr") %>% | |
| map_dfr(~{ | |
| date <- .x %>% html_nodes("td:nth-child(1)") %>% html_text(T) %>% paste(., " 2020") %>% as.Date("%b. %d %Y") | |
| total <- .x %>% html_nodes("td:nth-child(2)") %>% html_text(T) %>% parse_number() | |
| tibble(date, total) | |
| }) | |
| bind_rows( | |
| WHO_sars_totals %>% | |
| mutate(days = date - as.Date("2002-11-27")) %>% | |
| bind_rows(tibble(days = 0, total = 0),.) %>% | |
| filter(total <= 8096 & days <= 200) %>% | |
| complete(days = full_seq(days, 1)) %>% | |
| mutate(total = na.locf(total), virus = "SARS"), | |
| covid_totals %>% | |
| mutate(days = date - as.Date("2019-12-01")) %>% | |
| bind_rows(tibble(days = 0, total = 0),.) %>% | |
| complete(days = full_seq(days, 1)) %>% | |
| mutate(total = na.locf(total), virus = "Covid-19") | |
| ) %>% | |
| ggplot(aes(days, total, col = virus)) + | |
| geom_step(direction = "hv", size = 0.8) + | |
| geom_point(data = . %>% group_by(virus) %>% top_n(1, days)) + | |
| geom_text(data = . %>% group_by(virus) %>% top_n(1, days), aes(label = paste0(" ",virus)), hjust=0, family = "Open Sans", fontface = "bold") + | |
| theme_minimal() + | |
| theme( | |
| plot.title.position = "plot", | |
| plot.title = element_textbox_simple( | |
| size = 13, | |
| lineheight = 1.2, | |
| margin = margin(5, 0, 5.5, 0), | |
| padding = margin(0,0,8,0) | |
| ), | |
| axis.title.x = element_textbox_simple( | |
| size = 10, | |
| lineheight = 1.2, | |
| margin = margin(5, 0, 5.5, 0), | |
| padding = margin(0,0,8,0), | |
| hjust = 0.5 | |
| ), | |
| panel.grid.minor = element_blank(), | |
| panel.grid.major.x = element_blank(), | |
| panel.grid.major.y = element_line(color = c("black", rep("gray90", 10))), | |
| axis.ticks.x = element_line(), | |
| legend.position = "none", | |
| plot.margin = unit(c(2,15,2,2), "mm"), | |
| text = element_text(family = "Open Sans"), | |
| axis.title.y = element_blank(), | |
| plot.caption.position = "plot", | |
| plot.caption = element_textbox_simple( | |
| size = 8, | |
| lineheight = 1.1, | |
| margin = margin(0, 0, 0, 0), | |
| padding = margin(7,0,0,0), | |
| hjust=0 | |
| ) | |
| ) + | |
| scale_colour_manual(values = c("red", "cyan3")) + | |
| coord_cartesian(clip = "off") + | |
| scale_x_continuous(expand = c(0,0)) + | |
| scale_y_continuous(expand = c(0,0), labels = label_comma()) + | |
| labs(x = "Days since outbreak began <span style='font-family: Arial'>→</span>", y = "", title = "<b style='font-weight:bold; color:red'>Covid-19 (Coronavirus)</b> has infected\n far more people than <b style='font-weight:bold; color:cyan3'>SARS</b> did at the same stage", caption = "Sources: WHO; Worldometer") | |
| ggsave("covid.png", scale=2, width = 7, height = 5, units = "cm") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment