Generalized Correlates Analysis Reporting

Summary

This repository houses modular workflows for statistical analyses of correlates of risk / protection and automated reporting of analytic results. It serves as a generalized suite of tools, based on the analyses originally designed for the USG Biostatistics Response Team's analysis of COVID-19 vaccine efficacy trials (archived here). See below for brief descriptions of each of the analysis modules. This repository is designed as the second part of an analytic pipeline, with the correlates processing module serving as an upstream component.

Note: automated builds of the correlates of risk and protection analyses are evaluated by the Travis CI continuous integration service and the PDF reports posted to this repository's gh-pages branch.

List of Analysis Modules

• Correlates of Risk (CoR) Analyses
  • cor_coxph: Cox proportional hazards modeling of risk.
  • cor_tabular: Tabular descriptions of correlates of risk.
  • cor_graphical: Graphical descriptions of correlates of risk.
  • cor_threshold: Risk modeling based on correlate thresholds.
  • cor_nonlinear: Nonlinear modeling and evaluation.
  • cor_surrogates: Optimal surrogates analyses.
• Correlates of Protection (CoP) Analyses
  • cop_prinstrat: Principal stratification analyses.
  • cop_stochastic: Stochastic risk and vaccine efficacy evaluation.
  • cop_mediation: Correlate-mediated vaccine efficacy and risk.

Instructions for Use

• All analysis code are written in R and we use renv to manage package versions.
• After cloning the repo, start R in the root directory. Enter

renv::restore()

to install package dependencies. Installation may take a few hours depending on internet speed. If renv errors occur, check to make sure that under the home directory there is no .Rprofile or libs.

• To run the analyses of a specific module on a dataset, enter the module, specify the TRIAL label corresponding to the dataset, and run Make, e.g.

cd cor_coxph
export TRIAL=janssen_pooled_partA
make

The dataset corresponding to janssen_pooled_partA can be found in the config.yml file at the repo root.

Reproducibility Guide for Investigators Contributing Modules

• Portability: One should be able to move the code to a new location and run it. Consider using here to help achieve protability.

• The location of the analysis data file should be in a single place in the whole module, most typically in a config.yml file (used through the R config package).

• The versions of R and packages used should be managed with renv.

• Either a Makefile or a bash script should be included so that the analyses and report generation can be run with a single command.

---

License

The contents of this repository are distributed under the GPL-3 license. See file LICENSE.md for details.