Covid 7-Tage-Inzidenz nach Altersgruppen (https://twitter.com/matschnetzer/status/1455938384925450240?s=20)

covidheat.R

library(tidyverse)
library(lubridate)
library(msthemes)
library(patchwork)

# Get Covid data by age here: https://www.data.gv.at/katalog/dataset/3765ed62-0f9d-49ad-83b0-1405ed833108
# And vaccination data here: https://www.ages.at/themen/krankheitserreger/coronavirus/

cov <- read_csv2("CovidFaelle_Altersgruppe.csv") %>%
  mutate(Time = as.Date(Time, "%d.%m.%Y"))

cdat <- cov %>% filter(Bundesland == "Österreich") %>%
  group_by(Time, Altersgruppe, AltersgruppeID) %>%
  summarise(fall = sum(Anzahl), ew = sum(AnzEinwohner)) %>%
  group_by(Altersgruppe) %>%
  mutate(inzidenz = (fall-lag(fall,7))/ew*1e5) %>%
  drop_na()

impf <- bind_rows(read_csv2("Inzidenz_Impfstatus_12bis17Jahre.csv", col_names=F) %>% 
                    mutate(Alter = "12-17"),
                  read_csv2("Inzidenz_Impfstatus_18bis59Jahre.csv", col_names=F) %>%
                    mutate(Alter = "18-59"),
                  read_csv2("Inzidenz_Impfstatus_60plus.csv", col_names=F) %>%
                    mutate(Alter = "60+")) %>%
  select(Time = X1, Geimpft = X2, Ungeimpft = X3, Alter) %>%
  mutate(Time = as.Date(Time, "%d.%m.%Y"), 
         Alter = factor(Alter, levels = c("60+","18-59","12-17")),
         across(c(Geimpft,Ungeimpft), ~str_replace_all(., ",", "."))) %>%
  drop_na() %>%
  pivot_longer(cols = c(Geimpft, Ungeimpft), names_to = "Impfstatus", values_to = "Inzidenz", values_transform = list(Inzidenz = as.numeric))
  

full <- cdat %>% 
  ggplot(aes(x = Time, y = reorder(Altersgruppe, AltersgruppeID), fill = inzidenz)) +
  geom_tile() +
  scale_y_discrete(expand = c(0,0)) +
  scale_x_date(date_breaks = "2 months", expand = c(0,0), date_labels = "%b %y") +
  geom_rect(aes(xmin= as.Date("2021-08-01"), xmax = today()-1, ymin=-Inf, ymax=Inf), color = "black", fill = NA, size = 0.3) +
  #  geom_rect(aes(xmin= as.Date("2020-07-01"), xmax = max(cdat$Time)-years(1), ymin=-Inf, ymax=Inf), color = "black", fill = NA, size = 0.1) +
  scale_fill_viridis_c(option = "magma", direction = -1, limits = c(0,1200),
                       guide = guide_colorbar(title = "",
                                              title.vjust = 0.5, barwidth = 15,
                                              barheight = 0.5, ticks = F, 
                                              label.theme = element_text(size = 9, family = "Raleway"))) +
  labs(x="", y="")


short <- cdat %>% 
  filter(Time >= "2021-08-01") %>%
  ggplot(aes(x = Time, y = reorder(Altersgruppe, AltersgruppeID), fill = inzidenz)) +
  geom_tile(size = 0.15, color = "white") +
  scale_y_discrete(expand = c(0,0)) +
  scale_x_date(date_breaks = "1 month", expand = c(0,0), date_labels = "%d. %b") +
  scale_fill_viridis_c(option = "magma", direction = -1, limits = c(0,1200),
                       guide = guide_none()) +
  labs(x="", y="")

vacc <- impf %>%
  filter(Time >= "2021-08-01") %>%
  ggplot(aes(x = Time, y = Impfstatus, fill = Inzidenz)) +
  geom_tile(size = 0.15, color = "white") +
  scale_y_discrete(expand = c(0,0)) +
  scale_x_date(date_breaks = "1 month", expand = c(0,0), date_labels = "%d. %b") +
  scale_fill_viridis_c(option = "magma", direction = -1, limits = c(0,1200),
                       guide = guide_none()) +
  labs(x="", y="") +
  facet_wrap(~Alter, nrow = 3, strip.position = "left")


final <- full / ( short + vacc) +
  plot_layout(guides = "collect", widths = c(3,1)) +
  plot_annotation(title = "Entwicklung 4. Corona-Welle in Österreich",
                  subtitle = "7-Tage-Inzidenz nach Altersgruppen und Impfstatus",
                  caption = "Daten: AGES/EMS. Grafik: @matschnetzer") &
  theme_ms(alttf = T) +
  theme(axis.ticks.x = element_line(size = 0.1), 
        strip.background = element_rect(fill = "grey97", size = 0),
        strip.text = element_text(size = 7, hjust = 0.5, margin = margin(3,3,3,3)),
        axis.text.x = element_text(size = 7, hjust = 0.5),
        axis.text.y = element_text(size = 7, vjust = 0.5),
        legend.position = "bottom")

ggsave(final, filename = "covidheatlarge.png", dpi = 320, width = 8, height = 6)