In AnthonyEbert/COVID19data: What the Package Does (One Line, Title Case)

library(COVID19data)
library(dplyr)
library(ggplot2)

x = all_countries()

y = x %>% 
  filter(alpha3 == "ITA", Province.State %in% c("Emilia-Romagna", "Lombardia", "total")) %>%
  select(Province.State, date, confirmed, tested) %>%
  group_by(Province.State, weekday = lubridate::wday(date, label = T, abbr = F)) %>%
  mutate(
    diff_confirmed = c(first(confirmed), diff(confirmed)), 
    diff_tested = c(first(tested), diff(tested)),
    weeknum = lubridate::week(date)
  ) %>%
  mutate(
    diff_confirmed = pmax(diff_confirmed, 1e-1)
  )

y2 = y %>%
  group_by(Province.State) %>%
  filter(date > "2020-03-01") %>%
  mutate(smoothed_confirmed = exp(loess(log(diff_confirmed) ~ as.numeric(date), span = 0.45) %>% predict())) %>%
  mutate(epsilons = (diff_confirmed - smoothed_confirmed)/(smoothed_confirmed)) %>%
  mutate(epsilons = ifelse(is.finite(epsilons), epsilons, NA))

ggplot(y2) + aes(x = date, y = smoothed_confirmed, col = Province.State) + geom_line() + geom_point(aes(y = diff_confirmed))

ggplot(y2) + 
  aes(x = weekday, y = epsilons) +
  geom_boxplot() + 
  facet_wrap(~Province.State, ncol = 1)

AnthonyEbert/COVID19data documentation built on June 26, 2020, 6:51 a.m.