In seabbs/AssessBCGPolicyChange: Assess the Evidence Used to Motivate the 2005 Change in BCG Vaccination Policy

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Reassessing the evidence for universal school-age Bacillus Calmette Guerin (BCG) vaccination in England and Wales: re-evaluating and updating a modelling study


Sam Abbott, Hannah Christensen, Ellen Brooks-Pollock

Objectives

In 2005, England and Wales switched from universal BCG vaccination against tuberculosis (TB) disease for school-age children to targeted vaccination of neonates. We aimed to recreate and re-evaluate a previously published model, the results of which informed this policy change.

Design

We recreated an approach for estimating the impact of ending the BCG schools scheme, correcting a methodological flaw in the model, updating the model with parameter uncertainty, and improving parameter estimates where possible. We investigated scenarios for the assumed annual decrease in TB incidence rates considered by the UK’s Joint Committee on Vaccination and Immunisation and explored alternative scenarios using notification data.

Setting

England and Wales.

Outcome measures

The number of vaccines needed to prevent a single notification, and the average annual additional notifications caused by ending the policy change.

Results

The previously published model was found to contain a methodological flaw and to be spuriously precise. It greatly underestimated the impact of ending school-age vaccination compared to our updated, corrected, model. The updated model produced predictions with wide confidence intervals when parameter uncertainty was included. Model estimates based on an assumption of an annual decrease in TB incidence rates of 1.9% were closest to those estimated using notification data. Using this assumption, we estimate that 1600 (2.5,97.5% Quantiles (Q): 1300, 2000) vaccines would have been required to prevent a single notification in 2004.

Conclusions

The impact of ending the BCG schools scheme was found to be greater than previously thought when notification data were used. Our results highlight the importance of independent evaluations of modelling evidence, including uncertainty, and evaluating multiple scenarios when forecasting the impact of changes in vaccination policy.

Reproducibility

Repository structure

The repository is structured as an R package. It has the following structure:

• data-raw: Raw data processing.
• data: Processed data.
• R: Supporting R functions.
• docs: Documentation for R code.
• vignettes: Analysis paper, results, and analysis plan.
• peer-review: Documentation required for peer review.

Manual install

• Install R (analysis run with 3.5.2) and Rstudio (alternatively use Docker as outlined below).

• Download the analysis folder from https://github.com/seabbs/AssessBCGPolicyChange/archive/master.zip or use git clone, as follows, in the command line (not the R terminal).

```{bash clone-package, eval = FALSE} git clone https://github.com/seabbs/AssessBCGPolicyChange.git

- Once this has been downloaded click on the project file (`AssessBCGPolicyChange.Rproj`).

- Install the analysis dependencies and build the package using the following. To enable more robust reproducibility consider using the [`checkpoint`](https://cran.r-project.org/web/packages/checkpoint/index.html) package versioned locked to R `3.5.2`.

```r
#install.packages("devtools")
# To build locally
devtools::install_dev_deps(dependencies = TRUE)
devtools::install()
# Alternatively to remote install
devtools::install_github("seabbs/AssessBCGPolicyChange", dependencies = TRUE)

• Load the analysis results by running vignettes/paper.Rmd. Alternatively the complete analysis (along with documentation) can be reconstructed using make in the project root directory.

• See data-raw for data processing and the documentation for implementation details.

Docker

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

```{bash, eval = FALSE} docker run -d -p 8787:8787 --name assessbcgpolicychange -e USER=assessbcgpolicychange -e PASSWORD=assessbcgpolicychange seabbs/assessbcgpolicychange

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

If you have access to the required underlying raw data (see [`tbinenglanddataclean`](https://www.samabbott.co.uk/tbinenglanddataclean/)) then the entire analysis can be reproduced from scratch by adding the following to the `docker run` command, with the data saved into `data/tb_data`. The data requirements, and structure, can be found [here](https://www.samabbott.co.uk/tbinenglanddataclean/).

```{bash, eval = FALSE}
--mount type=bind,source=$(pwd)/data/tb_data,target=/home/DirectEffBCGPolicyChange/data/tb_data

Alternatively the analysis environment can be accessed via binder.

seabbs/AssessBCGPolicyChange documentation built on Dec. 24, 2019, 11:56 a.m.