# Load data (source: https://github.com/CSSEGISandData/COVID-19): 

library(tidyverse)
library(lubridate)
library(countrycode)

link1 <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv"
link2 <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv"


link1 %>% 
  read_csv() %>% 
  rename(Province = `Province/State`, Country = `Country/Region`) %>% 
  gather(Date, Recovered, -Province, -Country, -Lat, -Long) %>% 
  mutate(Date = mdy(Date)) -> df_recovered


link2 %>% 
  read_csv() %>% 
  rename(Province = `Province/State`, Country = `Country/Region`) %>% 
  gather(Date, Confirmed, -Province, -Country, -Lat, -Long) %>% 
  mutate(Date = mdy(Date)) -> df_confirmed


end_date <- ymd("2020-03-05")


df_recovered %>% 
  filter(Date == end_date) %>% 
  group_by(Country) %>% 
  mutate(TotalRec = sum(Recovered)) %>% 
  ungroup() %>% 
  filter(!duplicated(Country)) %>% 
  select(Country, TotalRec) -> recovered_0503



df_confirmed %>% 
  filter(Date == end_date) %>% 
  group_by(Country) %>% 
  mutate(TotalCon = sum(Confirmed)) %>% 
  ungroup() %>% 
  filter(!duplicated(Country)) %>% 
  select(Country, TotalCon) -> confirmed_0503


full_join(confirmed_0503, recovered_0503, by = 'Country') %>% 
  mutate(N_cases = TotalCon - TotalRec) -> df_final



df_final %>% 
  mutate(Country = case_when(Country %in% c("Mainland China", "Macau", "Hong Kong") ~ "China", 
                             Country == "US" ~ "United States", 
                             Country == "UK" ~ "United Kingdom", 
                             TRUE ~ Country)) %>% 
  group_by(Country) %>% 
  summarise(N_cases = sum(N_cases)) %>% 
  ungroup() %>% 
  mutate(iso3 = countrycode(Country, origin = "country.name", destination = "iso3c")) -> df_final



library(highcharter)

highchart(type = "map") %>% 
  hc_add_series_map(map = worldgeojson, df = df_final, value = "N_cases", joinBy = "iso3") %>% 
  hc_colorAxis(stops = color_stops()) %>% 
  hc_title(text = "Corona Virus Prevalence by Country as of 05-03-2020", 
           style = list(fontSize = "24px")) %>% 
  hc_credits(enabled = TRUE, style = list(fontSize = "12px"),  
             text = "Source: Johns Hopkins University Center for Systems Science and Engineering") %>% 
  hc_tooltip(useHTML = TRUE, headerFormat = "",
             pointFormat = "Country: {point.Country}, Number of Corona Cases: {point.N_cases}") %>% 
  hc_add_theme(hc_theme_flatdark())

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