index_cor.Rmd

---
knit: "bookdown::render_book"
title: "COVID-19 Correlates of Risk Analysis Report"
subtitle: '`r source(here::here("_common.R")); paste(study_name, "Study")`'
author: "USG COVID-19 Response Biostatistics Team"
date: "`r format(Sys.time(), '%B %d, %Y')`"
documentclass: book
site: bookdown::bookdown_site
bibliography: [book.bib, packages.bib]
biblio-style: apalike
suppress-bibliography: true
link-citations: yes
colorlinks: yes
graphics: yes
lot: yes
lof: yes
always_allow_html: yes
header-includes:
   - \usepackage{eso-pic,graphicx,transparent,caption,pdflscape,titling} # keep titling last!
   - \usepackage[margin=1in]{geometry}
   - \usepackage{float}
   - \usepackage{subfig}
---




```{r, include = knitr::is_latex_output() & startsWith(study_name, "Mock")}
knitr::asis_output("\\AddToShipoutPictureFG{
  \\AtPageCenter{
    \\makebox[0pt]{\\rotatebox[origin=c]{45}{
      \\scalebox{10}{\\texttransparent{0.3}{MOCK}}}}}}")
```

# Disclaimers


The data presented in the analysis are provided to NIAID in accordance with Clinical Trial Agreement between the parties. The study was funded in part by BARDA under Government Contract No. 75A50120C00034.


<!-- `r if ( !( grepl("moderna", attr(config::get(config = Sys.getenv("TRIAL")), "config") ) ) )'<!--'` -->


<!-- * The data presented in the analysis originated from the Moderna Sponsored mRNA-1273-P301 clinical study and are provided to NIAID in accordance with Clinical Trial Agreement between the parties. The study was funded in part by BARDA under Government Contract No. 75A50120C00034 -->

<!-- * The preliminary immunogenicity data presented here do not reflect the Sponsors statistical analysis plan and therefore should not be interpreted as a protocol defined read-out of the clinical study. -->

<!-- * These data are not to be disclosed without written permission of Moderna. -->

\textbf{Statistical Analysis Plan}

The SAP is available at https://doi.org/10.6084/m9.figshare.13198595

\textbf{Reproducibility Notice}

This project integrates the virtual environments framework provided by [the
`renv` package](https://rstudio.github.io/renv/) for computational
reproducibility. By taking this approach, all results are generated using a
consistent versioning of both R and several R packages. This version of the
report was built with `r R.version.string`, [pandoc](https://pandoc.org/)
version `r rmarkdown::pandoc_version()`, and the following R packages:

```{r pkg-list, echo=FALSE, results="asis"}
# borrowed from https://github.com/tidymodels/TMwR/blob/master/index.Rmd
deps <- desc::desc_get_deps()
pkgs <- sort(deps$package[deps$type == "Imports"])
pkgs <- sessioninfo::package_info(pkgs, dependencies = FALSE)
df <- tibble::tibble(
  package = pkgs$package,
  version = pkgs$ondiskversion,
  source = gsub("@", "\\\\@", pkgs$source)
)
knitr::kable(df, format = "markdown")
```

To get started with using this project and its `renv` package library, we
first recommend briefly reviewing the [`renv` collaboration
guide](https://rstudio.github.io/renv/articles/collaborating.html).