rus_male_mortality.R

###############################################################################
#
# Sex ratios 29-10-2016
# HMD data: illustrate Russian male mortality specifics 
# Ilya Kashnitsky, [email protected]
#
################################################################################

# load required packages
library(dplyr) # version 0.5.0
library(ggplot2) # version 2.1.0
library(HMDHFDplus) # version 1.1.8


# Read HMD data directly into R
# please note! the arguments "ik_user_hmd" and "ik_pass_hmd" are my login credidantials
# at the website of Human Mortality Database, which are stored locally at my computer. 
# In order to access the data, you need to create an account at
# http://www.mortality.org/
# and provide your own credidantials to the `readHMDweb()` function

# load LT for men, RUS and JPN
rus <- readHMDweb('RUS',"mltper_1x1",ik_user_hmd,ik_pass_hmd)
jpn <- readHMDweb('JPN',"mltper_1x1",ik_user_hmd,ik_pass_hmd)

# compare mortality rates for 2014
ru <- rus %>% filter(Year == 2014) %>% transmute(age=Age,rus=mx)
jp <- jpn %>% filter(Year == 2014) %>% transmute(age=Age,jpn=mx)
df <- left_join(jp,ru,'age') %>% mutate(ru_rate=rus/jpn)

# plot
gg <- ggplot(df, aes(age,ru_rate)) + 
        geom_hline(yintercept = 1, color = 'red') +
        geom_line(aes(group=1)) + 
        theme_minimal(base_size = 15) + 
        scale_y_continuous('mortality rate ratio',
                           breaks = 0:10, labels = 0:10, limits = c(0, 10)) +
        annotate('text',x=c(0, 55), y = c(1.75,5), label = c('Japan','Russia'),
                 color = c('red','black'), hjust = 0, vjust = 1, size = 7) +
        ggtitle('Compare age-specific mortality of males\nRussia and Japan, 2014, HMD')

ggsave('male_mortality_compare.png', gg, width = 10, height = 7, type = 'cairo-png')