italy_covid19_charts_20200406.R

library(covid19italy)
library(tidyverse)
library(scales)
library(ggthemes)
library(lubridate)
library(zoo)

update_data()

#get regional data

iregion <- italy_region %>%
  arrange(region_name,date) %>%
  group_by(region_name) %>%
  mutate(case_change = ifelse(date == min(date),cumulative_cases,cumulative_cases - lag(cumulative_cases)),
    case_growth = ifelse(date == min(date),0,(cumulative_cases - lag(cumulative_cases))/lag(cumulative_cases)),
         death_growth = ifelse(date == min(date),0,(death - lag(death))/lag(death)),
         daily_death = ifelse(date == min(date),death,death - lag(death)),
         rolling_positives = rollapply(case_change,7,mean,align='right',fill=NA),
         rolling_deaths = rollapply(daily_death,7,mean,align='right',fill=NA)) %>%
  ungroup()

quarantine_date = as_date('2020-03-08')
national_quarantine = as_date('2020-03-09')

lombardy <- iregion %>%
  filter(region_name == 'Lombardia') %>%
  mutate(quarantine_status = date >= quarantine_date)
  
#plot it
  
lplot <- lombardy %>%
  filter(!is.na(rolling_positives)) %>%
  ggplot(aes(x=date,y=rolling_positives))+
  geom_line()+
  scale_y_continuous(labels = comma)+
  scale_x_date()+
  theme_tufte()+
  ggtitle('Lombardy: COVID-19 rolling 7-day average for new confirmed cases')+
  xlab('Date') +
  ylab('Cases')+
  geom_vline(xintercept = quarantine_date,linetype=2,alpha=0.5)+
  geom_text(aes(x=quarantine_date, label="\nregional quarantine", y=1000), colour="black", angle=90, text=element_text(size=9))

#southern version

mg <- c('Abruzzo','Basilicata','Calabria','Campania','Molise','Puglia','Sicilia')

mg_plot <- iregion %>%
  filter(!is.na(rolling_positives)) %>%
  filter(region_name %in% mg) %>%
  ggplot(aes(x=date,y=rolling_positives,col=region_name))+
  geom_line()+
  scale_y_continuous(labels = comma)+
  scale_x_date()+
  theme_tufte()+
  ggtitle('Southern Italy: COVID-19 rolling 7-day average for new confirmed cases')+
  xlab('Date') +
  ylab('Cases')+
  labs(col='Region')+
  geom_vline(xintercept = quarantine_date,linetype=2,alpha=0.5)+
  geom_text(aes(x=national_quarantine, label="\nnational quarantine", y=100), colour="black", angle=90, text=element_text(size=9))