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_tabular: Tabular descriptions of correlates of risk.
  • cor_graphical: Graphical descriptions of correlates of risk.
  • cor_coxph: Cox proportional hazards modeling 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.

• Pdf reports are generated by shell scripts. For example, to run two mocks report, enter

bash test_before_submit cor_coxph

which creates two pdf files under the cor_coxph directory. The process takes about 30 min to a few hours to run depending on the number of available CPUs.

Collaboration Guide

• Getting started: see our contribution guidelines.
• Code style guide, with some modifications; this will largely be enforcd with styler.
• Project organization: mostly independent subdirectories, each incorporating here for path resolution.
• Package version control and virtual environments using renv.

---

License

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