Time-trends in life expectancy of people with severe mental illness in Scotland, 2000-2019: a population-based study

This repository accompanies the paper:

Fleetwood K, Alotaibi R, Scheuer SH, Smith D, Wild SH, Jackson CA. Time-trends in life expectancy of people with severe mental illness in Scotland, 2000-2019: a population-based study. (submitted for peer review)

It includes the following R scripts:

01_data.R

• Reads in the SMR04 records
• Reads in the death records
• Identifies people with schizophrenia, bipolar disorder or depression, based on the SMR04 records
• Identifies the cohort
• Creates the baseline characteristics tables

02_calculate_lyl.R

• Loads the data output from 01_data.R
• Loads the Scottish national lifetables
• Uses the R package lillies (https://cran.r-project.org/web/packages/lillies/index.html) to calculate life years lost, excess life years lost and survival curves

03_lyl_plot.R

• Loads the data output from 02_calculate_lyl.R
• Creates the life years lost plot (figure 2)

04_excess_lyl_plot.R

• Loads the data output from 02_calculate_lyl.R
• Creates the excess life years lost plot (figure 3)

05_survival_plot.R

• Loads the data output from 02_calculate_lyl.R
• Creates the survival curves plot (figure 4)