Model Tuberculosis, including BCG vaccination, in England

ModelTBBCGEngland is an R package that contains models, summarised data, and fitting scripts for a model of TB, including BCG vaccination, fit to routine surveillance data in England.

Installation

You can install ModelTBBCGEngland directly from github with:

# install.packages("devtools")
devtools::install_github("seabbs/ModelTBBCGEngland")

Model development

For a discussion of the model development process please see here. For a discussion of the model fitting pipeline please see here.

Model fitting

Run the following code in the terminal after installing and building the package and opening the Rstudio project. The results (and logs) will be found at ./vignettes/results.

nohup Rscript inst/scripts/run-scenarios.R --sample_priors --fit --reports

To fit only the main scenario add --scenario baseline. If interested in rapid exploration or if using limited compute resources experiment with the --calib_run flag which uses point estimates for the initial conditions and process noise - reducing the number of particles required. Alternatively explore the other options available using --help. An example of a fitting run used for exploration is below.

nohup Rscript inst/scripts/run-scenarios.R --sample_priors --fit --reports --cores 16 --calib_run --scenario baseline

For more interactive testing see ./tests/manual-tests/test-rbi-fit.R. This script was used during pipeline development.

Using docker

This analysis was developed in a docker container based on the tidyverse docker image. To run the docker image run:

docker run -d -p 8787:8787 -e USER=ModelTBBCGEngland -e PASSWORD=ModelTBBCGEngland \
    --mount type=bind,source=$(pwd)/results/modeltbbcgengland,target=/home/rstudio/ModelTBBCGEngland/vignettes/results \
    --mount type=bind,source=$(pwd)/data/tb_data,target=/home/rstudio/ModelTBBCGEngland/data-raw/tb_data \
    --name modeltransvsdirect seabbs/modeltbbcgengland

This command expects both a data and results folder to be available to be mounted. Create them using the following (Mac/Linux).

mkdir -p results/modeltbbcgengland
mkdir -p data/tb_data

The rstudio client can be found on port :8787 at your local machines ip. The default username:password is seabbs:seabbs, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere.

To run a plain R terminal use:

docker run --rm -it --user seabbs modeltbbcgengland /usr/bin/R

To run a plain bash session:

docker run --rm -it --user seabbs modeltbbcgengland /bin/bash