Explore TB mortality excluding HIV using getTBinR

explore_tb_mortality_exc_hiv

# install.packages("getTBinR")
library(getTBinR)
# install.packages("tidyverse")
library(tidyverse)

# Get the data
tb_burden <- get_tb_burden(download_data = TRUE, save = TRUE)
dict <- get_data_dict(download_data = TRUE, save = TRUE)

# Look up variables with mortality in their definition
search_data_dict(def = "mortality")

# Map mortality excluding HIV
map_tb_burden(metric = "e_mort_exc_tbhiv_100k")

# Get countries with highest TB mortality (exc HIV) in the data
high_mortality_countries <- tb_burden %>% 
  group_by(country) %>% 
  summarise(e_mort_exc_tbhiv_100k = max(e_mort_exc_tbhiv_100k)) %>% 
  ungroup %>% 
  arrange(desc(e_mort_exc_tbhiv_100k)) %>% 
  slice(1:10) %>% 
  pull(country) %>% 
  unique

# Overview of 10 countries with highest TB mortality rates (exc HIV)
plot_tb_burden_overview(metric = "e_mort_exc_tbhiv_100k",
                        countries = high_mortality_countries)


# Trends over time in mortality rates (exc HIV) by country
plot_tb_burden(metric = "e_mort_exc_tbhiv_100k",
               countries = high_mortality_countries,
               facet = "country", scales = "free_y")

# Trends over time in incidence rates by country for countries with highest TB mortality (exc HIV)
plot_tb_burden(countries = high_mortality_countries,
               facet = "country", scales = "free_y")