/correlates_processing

Generalized reproducible reporting workflow for immune correlates data processing in vaccine efficacy trials

Primary LanguageHTMLGNU General Public License v3.0GPL-3.0

Generalized Correlates Analysis Processing

Summary

This repository houses modular workflows for the processing of correlates of risk / protection data, exploratory tabular and graphical analyses of correlates immunogenicity, and the 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 first part of an analytic pipeline, with the correlates reporting module serving as a downstream component.

Build Status 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.

Contents

  • Immunogenicity Description
    • immuno_tabular: Tabular descriptions of marker immunogenicity.
    • immuno_graphical: Graphical descriptions of marker immunogenicity.
  • Baseline Risk Score Evaluation
    • riskscore_baseline: Super Learner baseline risk score for exposure.

Collaboration Guide

  • 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.
  • Code review procedure: see our contribution guidelines.

License

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