Data

Mortality from Chronic Diseases in Italy, France, and Spain

Overview

Data for this challenge comes from the hmsidwR package, which includes global polygon data for mapping disease burden (DALYs) worldwide and other health metrics.

Load Libraries and Data

library(tidyverse)
library(hmsidwR)
library(sf)

data(idDALY_map_data)
data(deaths9)

To gain more info about the data:

?idDALY_map_data
?deaths9

deaths <- deaths9 %>%
  filter(sex=="both") %>%
  select(location,cause,dx)

deaths %>%head

Combine Datasets by location

geometry <- idDALY_map_data  %>%
  select(location_name, geometry) 

deaths_map_data <- deaths %>%
  inner_join(geometry, 
            by = c("location" = "location_name"))
deaths_map_data %>% count(cause)

CamCorder and ShowText

# library(camcorder)
# camcorder::gg_record(width = 6, height = 4)

# Colours
text_col <- "grey10"
bg_col <- "grey95"

# Fonts from Google Fonts
# library(showtext)
# font_add_google("Metal Mania")
# font_add_google("Dancing Script")
# showtext_auto()
# showtext_opts(dpi = 300)
# title_font <- "Metal Mania"
# body_font <- "Dancing Script"

base_map <- idDALY_map_data %>%
  ggplot() +
  # Base map layer
  geom_sf(fill = NA, 
          color = alpha("grey70", 0.4), 
          linewidth = 0.2) +
  # Disease-specific data layer
  geom_sf(data = deaths_map_data %>%
            filter(cause %in% c("Alzheimer's disease and other dementias",
                                "Chronic obstructive pulmonary disease",
                                "Diabetes and kidney diseases",
                                "Stroke")),
          aes(fill = dx, geometry = geometry),
          color = alpha("grey70", 0.4), 
          linewidth = 0.2) +
    # Coordinate limits (Europe focus)
  coord_sf(xlim = c(-5, 20), 
           ylim = c(35, 56),
           expand = FALSE) 

base_map

facet_legend_map <- base_map +
  # Facets for each disease
  facet_wrap(~cause,
             labeller = label_wrap_gen(width = 25),
             strip.position = "bottom") +
  ggthemes::theme_map() +
  theme(legend.position = "top",
        legend.key.size = unit(0.8, "lines"),
        legend.title = element_text(size = 5, face="bold"),
        legend.text = element_text(size = 4),
        legend.background = element_rect(fill = NA,colour = NA))

facet_legend_map

colored_map <- facet_legend_map +
  # Color scale and legend
  scale_fill_viridis_c(name = "Deaths\n(per 100,000 people)",
                       labels = scales::label_number(scale = 1e-3),
                       option = "D", direction = -1) +
  theme(text = element_text(family = body_font,
                            size = 9,
                            color = text_col),
        strip.text = element_text(size = 7, face = "bold"),
        strip.background = element_rect(fill = NA, color = NA))

colored_map

ragg::agg_png("day4_my_data3.png",
              width = 6, height = 4, 
              units = "in", 
              res = 320,
              bg = bg_col)

colored_map

dev.off()