Reproducible Reports

39.1 Quarto (.qmd) — the modern standard

Quarto produces HTML, PDF (LaTeX/Typst), Word, PowerPoint, Reveal.js slides, websites, books, blogs, and dashboards; supports R, Python, Julia and Observable JS; cross-references, citations (BibTeX), callouts, tabsets, and interactive widgets.

---
title: "Penguin Report"
author: "Your Name"
date: today
format:
  html:
    toc: true
    code-fold: true
  pdf: default
  docx: default
execute:
  echo: true
  warning: false
params:
  species: "Adelie"
---

## Introduction

This report analyses **`r params$species`** penguins.

The mean mass is `r round(mean(penguins$body_mass_g, na.rm = TRUE))` g (see @fig-mass).

quarto render report.qmd
quarto render report.qmd -P species:Gentoo     # parameterized report
quarto preview report.qmd

39.2 R Markdown (.Rmd)

The predecessor (still widely used): rmarkdown::render("report.Rmd"). Chunk options: echo, eval, include, message, warning, fig.width, cache. Ecosystem: bookdown, blogdown, xaringan, flexdashboard, pagedown, distill.

39.3 Tables for reports

knitr::kable(head(mtcars))
gt::gt(head(mtcars)) |> gt::fmt_number(columns = mpg, decimals = 1) |> gt::tab_header(title = "Cars")
flextable::flextable(head(mtcars))          # great for Word/PowerPoint
gtsummary::tbl_regression(lm(mpg ~ wt, mtcars))
reactable::reactable(mtcars)                 # interactive HTML table
DT::datatable(mtcars, filter = "top")

39.4 Literate programming tips

Keep raw data read-only, compute everything in the document, set seeds, print sessionInfo() at the end, and render from a clean session.