COVID plot adapted from https://github.com/JonMinton/COVID-19

plot-corona.R

# FROM: https://github.com/JonMinton/COVID-19



DF = tidied_data %>% 
  filter(type == "confirmed") %>% 
  mutate(
    higher = case_when(
      higher == "Iran (Islamic Republic of)" ~ "Iran",
      higher == "Hong Kong SAR"  ~ "Hong Kong",
      higher == "Republic of Korea" ~ "South Korea",
      TRUE ~ higher
    )
  ) %>% 
  group_by(higher, date) %>% 
  summarise(n = sum(n)) %>% 
  ungroup() %>% 
  group_by(higher) %>% 
  arrange(date) %>% 
  filter(n >= 100) %>%
  mutate(first_date = date[1]) %>% 
  mutate(days_since_first = date - first_date) %>% 
  mutate(max_days_since_first = max(days_since_first)) %>% 
  ungroup() %>% 
  mutate(country = fct_reorder(higher, desc(max_days_since_first))) %>%
  filter(country != "Others") %>% 
  
  # Create label in the last day for each country
  group_by(country) %>% 
  mutate(
    name_end = 
      case_when(
        n == max(n) ~ paste0(as.character(country), " - ", days_since_first, " days"),
        TRUE ~ ""
      )
  )
  

DF_names <- DF %>% 
  # group_by(country) %>% 
  distinct(country) %>% 
  pull(country)



# PLOT --------------------------------------------------------------------

plot1 = DF %>% 
  ggplot(aes(x = days_since_first, y = n, color = country)) +
  geom_line() + 
  ggrepel::geom_label_repel(aes(label = name_end), show.legend = FALSE, segment.color = "grey", segment.size  = .3) + #, segment.linetype = 5 
  scale_y_log10(
    breaks = scales::trans_breaks("log10", function(x) 10^x),
    labels = scales::trans_format("log10", scales::math_format(10^.x))) + 
  labs(
    title = "Confirmed cases after first 100 cases",
    subtitle = "Arranged by number of days since 100 or more cases",
    x = "Days after 100 confirmed cases",
    y = "Confirmed cases (log scale)", 
    caption = "Source: Johns Hopkins CSSE"
  ) +
  theme_minimal() +
  theme(legend.position = "none")
  
  
ggsave("figures/days_since_100.png", plot1, height = 20, width = 20, units = "cm", dpi = 300)