afarx / mortality-statsmodel

Mortality using bayesian hierarchical modelling

mortality-statsmodel

Mortality modelling using Bayesian hierarchical models and statistical machine learning methods.

This code is used in

Rashid, T., Bennett, J.E. et al. (2021). Life expectancy and risk of death in 6791 communities in England from 2002 to 2019: high-resolution spatiotemporal analysis of civil registration data. The Lancet Public Health.

The parametric model code requires R version 3.6 or higher and the following packages:

• nimble (>= 0.11.1)
• tidyverse
• docopt
• here
• lme4
• geojsonio
• spdep

And the analysis code requires the further packages:

• reshape2
• rstan
• foreach
• doParallel

Parametric models

These are a collection of Bayesian hierarchical models in Models/parametric. Deaths are modelled using a negative binomial likelihood. We are looking at the death rate per person in a given spatial unit, year and age group stratum. It is the death rate per person that varies between models. The following model designs are used:

• The nested model is designed for a three-level nested spatial hierarchy. In our case it follows the ONS' hierarchical output area geographies. Each Lower layer Super Output Area (LSOA) lies within a Middle layer Super Output Area (MSOA), which lies within a Local Authority District (LAD) (can also be used with MSOA, LAD and region). The spatial effects are modelled as IID.
• The BYM model shares information between the nearest neighbours to each spatial unit.

The models here are fitted using nimble. For ease of reading and to aid the user more familiar with other MCMC software, I've also added the basic model structure as BUGS code.

An example invocation of the code from the command line is as follows:

Rscript run_model.R MSOA nested 1 10000 5000 --num_chains=4

For the full explanation of the options available, run

Rscript run_model.R --help

Data

The Mortality/ folder should hold the deaths data. Data used in the analysis are controlled by the Small Area Health Statistics Unit who do not have permission to release data to third parties. Individual mortality data can be requested through the Office for National Statistics. If you would like a file containing simulated numbers that allow you to test the code, please contact [e-mail].

The Inits/ folder contains inital values for the MCMC (made using the inits.R script). The GIS/ folder contains TopoJSON files for the LSOA/MSOA geographies and population-weighted LSOA/MSOA centroids, both available from the ONS' Open Geography Portal.