Deaths by week

code.R

# Deaths by week

options("max.print" = 1e4)

library(eurostat)
library(data.table)
library(ggplot2)
library(ISOcodes)

cntry <- as.data.table(ISO_3166_1)
cntry[, .(geo = Alpha_2, cntry = Name)]

# https://ec.europa.eu/eurostat/web/products-datasets/-/demo_r_mwk_ts
dat <- get_eurostat(id = "demo_r_mwk_ts")
setDT(dat)

dat
dat[, .N, keyby = .(sex)]
dat[, .N, keyby = .(unit)]

dat[, .N, keyby = .(geo)]
dat[, .N, keyby = .(time)]

dat[grepl("W99", time)]
dat <- dat[!grepl("W99", time)]

dat[, year := as.integer(substr(time, 1, 4))]
dat[, week := as.integer(substr(time, 6, 7))]

dat[week > 53]
dat[week > 52]

dat[, .N, keyby = .(year)]
dat[, .N, keyby = .(week)]
dcast.data.table(data = dat, formula = week ~ year, fun.aggregate = length)

dat[, y2020 := year == 2020L]

dat[geo == "EL", geo := "GR"]
dat[geo == "UK", geo := "GB"]

dat2 <- merge(dat, cntry[, .(geo = Alpha_2, cntry = Name)],
              by = "geo", all.x = T)

dat2[is.na(cntry), .N, keyby = .(geo, cntry)]

pl <- ggplot(data = dat2[sex == "T" & geo != "AD"],
             mapping = aes(x = week, y = values, group = year,
                           colour = y2020, alpha = year)) +
  geom_line() +
  scale_colour_brewer(palette = "Paired") +
  facet_wrap(~ cntry, scales = "free_y") +
  ggtitle("Deaths by week (total)", "Datasource: Eurostat [DEMO_R_MWK_TS]") +
  theme_bw()

ggsave(filename = "dths-by-wk.png", plot = pl, width = 16, height = 9)
ggsave(filename = "dths-by-wk.pdf", plot = pl, width = 16, height = 9)

Result: