Visualizing Cumulative Growth of COVID-19 Cases by Day

Mar 12, 2020 #eda #time-series

library(tidyverse)
library(plotly)

raw <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv")

df <- raw %>%
    select(-c(`Province/State`, Lat, Long)) %>% 
    rename(country = `Country/Region`) %>% 
    filter(!country %in% c("China", "Mainland China", "Others")) %>% 
    gather(date, cases, -country) %>% 
    mutate(date = as.Date(date, format = "%m/%d/%y")) %>% 
    group_by(country, date) %>% 
    summarise(cases = sum(cases)) %>% 
    ungroup()

split_by_country <- df %>% split(.$country)

ind <- split_by_country %>% 
    map_lgl(~ max(.x$cases, na.rm = TRUE) >= 100) %>% 
    which()
    
add_nday <- . %>% 
    arrange(date) %>% 
    filter(cases >= 100) %>% 
    mutate(nday = seq(1, length(date)))

pals = c(
    "US"                = "#374c80",
    "Korea, South"      = "#bc5090",
    "Singapore"         = "#ef5675",
    "Italy"             = "#ffa600",
    "Default"           = "#003f5c"
)

p <- split_by_country[ind] %>% 
    map(add_nday) %>% 
    bind_rows() %>% 
    mutate(
        col   = if_else(country %in% names(pals), country, "Default"),
        alpha = if_else(country %in% names(pals), 1, 0.9)
    ) %>% 
    ggplot(aes(nday, cases, col = col, alpha = alpha, group = country)) + 
    geom_line(show.legend = FALSE, size = 1.3) + 
    scale_y_log10(breaks = c(100, 200, 500, 1000, 2000, 5000, 10000)) + 
    scale_color_manual(values = pals) +
    coord_cartesian(xlim = c(1, 20)) + 
    theme_minimal(base_family = "Menlo", base_size = 11) + 
    labs(x = "", y = "")

ggplotly(p, tooltip = c("y")) %>%
    layout(
        title = list(
            text = paste0(
                'A True Test to Nation\'s Leadership & Crisis Management',
                '<br>',
                '<sup>',
                'COVID-19 cumulative growth since 100th case by day',
                '</sup>'
            ),
            x = 0, y = 0.98, xanchor = "left",
            font = list(size = 12)
        ),
       legend = list(orientation = "h", y = "0")
    )