##############################################################################
# File: tidycovid-logratios.R
#
# based on https://robjhyndman.com/hyndsight/logratios-covid19/
##############################################################################


# install.packages("devtools") # need this for install_github
library(devtools)

# install.packages("tidyverse")
library(tidyverse)

# install.packages("tsibble")
library(tsibble)

# See https://www.r-bloggers.com/meet-tidycovid19-yet-another-covid-19-related-r-package/

# install_github("joachim-gassen/tidycovid19")
library(tidycovid19)

#install.packages("ggthemes")
library(ggthemes)



# Download latest data
updates <- download_merged_data(cached = TRUE)

# Countries to highlight
countries <- c("SGP", "CHN", "USA", "KOR", "TWN", "JPN")

start_from_date <- as.Date("2020-02-01")

#
# Plot 1 - Confirmed cases (log scale) Y vs. Days after 100th confirmed case
#
updates %>%
  plot_covid19_spread(
    highlight = countries,
    type = "confirmed",
    edate_cutoff = 40
  )

#
# Plot 2 -  log ratios and plot them for each country
# with a smooth curve overlaid.
#
updates %>%
  mutate(cases_logratio = difference(log(confirmed))) %>%
  filter(
    iso3c %in% countries,
    date >= start_from_date
  ) %>%
  ggplot(aes(x = date, y = cases_logratio, col = country)) +
  geom_point() +
  geom_smooth(method = "loess") +
  facet_wrap(. ~ country, ncol = 3) +
  xlab("Date") +
  ggthemes::scale_color_colorblind()


#
# Plot 3 - Show only the smoothed log ratio
# (not the standard error band around it as in plot #2)
#
updates %>%
  mutate(
    cases_logratio = difference(log(confirmed))
  ) %>%
  filter(iso3c %in% countries) %>%
  filter(date >= start_from_date) %>%
  ggplot(aes(x = date, y = cases_logratio, col = country)) +
  geom_hline(yintercept = log(2)/c(2:7,14,21), col='grey') +
  geom_smooth(method = "loess", se = FALSE) +
  scale_y_continuous(
    "Daily increase in cumulative cases",
    breaks = log(1+seq(0,60,by=10)/100),
    labels = paste0(seq(0,60,by=10),"%"),
    minor_breaks=NULL
    #,
    #sec.axis = sec_axis(~ log(2)/(.),
    #                    breaks = c(2:7,14,21),
    #                    name = "Doubling time (days)")
  ) +
  ggthemes::scale_color_colorblind()