Coronavirus daily cumulative cases by type

coronavirus_daily_by_type.R

#---------------- Plotting Daily Cumulative Cases of the Coronavirus----------------
# Installing the most update version of the coronavirus
# install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")
data("coronavirus")


# Reformat and aggregate the data to daily by country and type of case
df_daily <- coronavirus %>% 
  dplyr::group_by(date, type) %>%
  dplyr::summarise(total = sum(cases, na.rm = TRUE)) %>%
  tidyr::pivot_wider(names_from = type,
                     values_from = total) %>%
  dplyr::arrange(date) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(active =  confirmed - death - recovered) %>%
  dplyr::mutate(confirmed_cum = cumsum(confirmed),
                death_cum = cumsum(death),
                recovered_cum = cumsum(recovered),
                active_cum = cumsum(active))

# plotting the data

plotly::plot_ly(data = df_daily) %>%
  plotly::add_trace(x = ~ date,
                    y = ~ active_cum,
                    type = "scatter",
                    mode = "lines+markers",
                    name = "Active",
                    line = list(color = "#1f77b4")) %>%
  plotly::add_trace(x = ~ date,
                    y = ~ recovered_cum,
                    type = "scatter",
                    mode = "lines+markers",
                    name = "Recovered",
                    line = list(color = "green"),
                    marker = list(color = "green")) %>%
  plotly::add_trace(x = ~ date,
                    y = ~ death_cum,
                    type = "scatter",
                    mode = 'lines+markers',
                    name = "Death",
                    line = list(color = "red"),
                    marker = list(color = "red")) %>%
  plotly::add_annotations(x = as.Date("2020-03-01"),
                          y = 42716,
                          text = paste("# of recovered cases surpass", 
                                       "<br>", 
                                       "the number of active cases"),
                          xref = "x",
                          yref = "y",
                          arrowhead = 5,
                          arrowhead = 3,
                          arrowsize = 1,
                          showarrow = TRUE,
                          ax = -270,
                          ay = 30) %>%
  plotly::layout(title = "",
                 yaxis = list(title = "Cumulative Number of Cases"),
                 xaxis = list(title = "Date"),
                 legend = list(x = 0.1, y = 0.9),
                 hovermode = "compare")