eurostat_data.R

## Eurostat amenamble mortality data

if(!require(eurostat))install.packages("eurostat")
library(eurostat)
library(tidyverse)
library(openxlsx)

## download table of contents
toc <- eurostat::get_eurostat_toc()

am <- search_eurostat("Amenable", type = "dataset")

am_data <- get_eurostat(id = "hlth_cd_apr")
am_data1 <- get_eurostat(id = "hlth_cd_apreu")

summary(am_data1)


write.xlsx(am_data, "eurostat_data.xlsx")
write.xlsx(am_data1, "eurostat_data1.xlsx")


am_data %>%
  filter(unit == "RT", values > 10) %>%
  ggplot(aes(time, values, shape = indic_he, colour = geo, group = geo)) + 
  geom_line() +
  geom_point() +
  facet_wrap(indic_he~icd10, scales = "free", nrow = 2) +
  labs(caption = "Source: EUROSTAT", 
       title = "Preventable and amenable mortality in Europe \n2010-2014")

  

am_data1 %>%
  filter(unit == "RT", values > 10, !icd10 == "TOTAL") %>%
  ggplot(aes(time, values, shape = indic_he, colour = icd10)) + 
  geom_line() +
  geom_point() +
  facet_wrap(indic_he~sex, nrow = 2) +
  labs(caption = "Source: EUROSTAT", 
       title = "Preventable and amenable mortality in Europe (EU28) \n2010-2014", 
       subtitle = "By ICD10 code", 
       y = "Rate") +
  scale_y_log10()


am_data2 <- get_eurostat(id = "hlth_cd_apr") %>% filter(time == max(time), unit == "RT") %>% mutate(cat = cut_to_classes(values, n = 5, decimals = 1))
mapdata <- merge_eurostat_geodata(am_data2, resolution = "20")

ggplot(mapdata, aes(x = long, y = lat, group = group)) +
  geom_polygon(aes(fill = cat), colour = "grey", size = .1) +
  labs(title = "Amenable mortality by NUTS-3 region, 2014",
       subtitle = "Mortality rate per 100,000", 
       fill = "Amenable mortality \nrate", 
       caption = "Source: EUROSTAT") +
  theme_void() +
  scale_fill_brewer(palette = "RdYlBu") + 
  coord_map(xlim = c(-12, 44), ylim = c(35,67)) 

ggsave("euro_am.png")