seabbs/modeltbbcgengland repository overview

⁠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