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10. R Markdown & Reproducible Reports

R Markdown is one of the most powerful features of R — it allows you to combine executable R code, narrative text, results, tables, figures, and references into a single document. The output can be HTML, PDF, Word, presentations, dashboards, websites, and more — all fully reproducible.

In 2026, Quarto has become the modern successor to R Markdown (recommended for new projects), but R Markdown is still widely used and supported.

10.1 Creating Dynamic Reports with R Markdown

Basic structure of an R Markdown (.Rmd) file

YAML

--- title: "My First Reproducible Report" author: "Anshuman" date: "March 2026" output: html_document --- # Introduction This is a sample report using R Markdown. ## Summary Statistics ```{r summary, echo=TRUE} summary(mtcars)

Visualization

language-{r

library(ggplot2) ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) + geom_point(size = 3) + geom_smooth(method = "lm") + labs(title = "Weight vs MPG by Cylinders")

text

How to create & render 1. In RStudio: File → New File → R Markdown → choose output format → OK 2. Write text in Markdown + code in `{r}` chunks 3. Click Knit button (or Ctrl+Shift+K) to render Key chunk options (very useful) ```r ```{r chunk-name, echo=FALSE, warning=FALSE, message=FALSE, fig.width=10, fig.height=6, eval=TRUE} # code here

text

- `echo = FALSE` → hide code, show only output - `warning = FALSE / message = FALSE` → hide warnings/messages - `fig.width / fig.height` → control figure size - `eval = FALSE` → don't run chunk (useful for setup) #### 10.2 Parameters, Tables, Figures & Citations Parameterized reports (run with different inputs) ```yaml --- title: "Sales Report" params: region: "North" year: 2025 ---

Use inside document:

R

# Sales for `r params$region` in `r params$year`

Beautiful tables

R

library(knitr) library(kableExtra) mtcars %>% head(10) %>% kbl(caption = "First 10 Rows of mtcars") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed"))

Figures with captions & references

R

```{r scatter-plot, fig.cap="Scatter plot of MPG vs Weight"} ggplot(mtcars, aes(wt, mpg)) + geom_point()

text

Citations & bibliography ```yaml --- bibliography: references.bib --- See @wickham2019 for more on tidyverse.

references.bib file example:

text

@book{wickham2019, title = {Advanced {R}}, author = {Wickham, Hadley}, year = {2019}, publisher = {Chapman and Hall/CRC} }

10.3 Converting to HTML, PDF, Word

HTML (default – interactive, fast)

YAML

output: html_document

PDF (professional, publication-ready)

YAML

output: pdf_document

Requires LaTeX (install TinyTeX: tinytex::install_tinytex())

Word (.docx)

YAML

output: word_document

Multiple formats at once

YAML

output: html_document: default pdf_document: default word_document: default

Custom themes & CSS

YAML

output: html_document: theme: cosmo # or cerulean, journal, flatly, darkly, etc. highlight: tango css: styles.css

10.4 Quarto – The Modern Replacement (2026 Standard)

Quarto (released by Posit in 2022) is the next-generation successor to R Markdown. It supports R, Python, Julia, and Observable — one tool for all.

Key advantages over R Markdown (2026)

• Unified syntax across languages

• Better PDF output (native LaTeX control)

• Built-in support for interactive plots, code folding, tabs, callouts

• Freeze computation (cache results)

• Websites, books, presentations, manuscripts from one source

Basic Quarto document (.qmd)

YAML

--- title: "My Quarto Report" author: "Anshuman" format: html: default pdf: default execute: echo: true warning: false --- # Introduction This is a Quarto document. ## Summary ```{r} summary(mtcars)

Plot

language-{r}

#| label: mpg-plot #| fig-cap: "MPG vs Weight" #| fig-width: 8 #| fig-height: 5 ggplot(mtcars, aes(wt, mpg)) + geom_point() + geom_smooth(method = "lm")

text

Render Quarto ```bash quarto render document.qmd # or in RStudio: click Render button

Quarto features you should know

• Callouts: ::: {.callout-note} … :::

• Tabs: ::: {.panel-tabset}

• Code folding: code-fold: true

• Cross-references: @fig-mpg-plot

• Citation: @wickham2019

Recommendation (2026):

• Use Quarto for all new work

• Keep R Markdown only for legacy projects or when Quarto is not yet supported

Mini Summary Project – Reproducible Report Create a new .qmd file in RStudio:

YAML

--- title: "Titanic Survival Analysis" format: html execute: echo: false warning: false --- ```{r setup} library(tidyverse) library(knitr)

Data Overview

language-{r}

titanic <- titanic::titanic_train kable(head(titanic))

Survival by Class

language-{r}

#| fig-cap: "Survival Rate by Passenger Class" titanic %>% ggplot(aes(x = factor(Pclass), fill = factor(Survived))) + geom_bar(position = "fill") + labs(x = "Class", y = "Proportion")

text

This completes the full R Markdown & Reproducible Reports section — now you can create dynamic, professional, fully reproducible reports and publications in R! Let me know the next section number (e.g., 11. Real-World Projects & Portfolio Building) or i

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