RMarkdown Reader for Obsidian

An Obsidian plugin that lets you browse, read, and edit RMarkdown (.rmd / .Rmd) files directly within your vault — without converting them to .md.

Features

• File explorer integration — .rmd files appear in the sidebar and can be opened like any other note
• Full editor support — edit .rmd files using Obsidian's markdown editor; files stay as .rmd
• R code chunk display — reading view shows a labeled header bar above each code chunk with the engine (R, Python, SQL, etc.), chunk name, and options
• Inline R code badges — inline R expressions (`r expr`) are visually marked with an R badge in reading view
• Search & graph — .rmd files are indexed by Obsidian and appear in search results and the graph view
• Theme-aware — all styling uses Obsidian CSS variables, so it adapts to any theme

Installation

From Obsidian Community Plugins (recommended)

1. Open Settings → Community Plugins → Browse
2. Search for "RMarkdown Reader"
3. Click Install, then Enable

Manual Installation

1. Download main.js, manifest.json, and styles.css from the latest release
2. Create a folder: <your-vault>/.obsidian/plugins/rmarkdown-reader/
3. Copy the three files into that folder
4. Restart Obsidian and enable the plugin in Settings → Community Plugins

How It Works

The plugin registers .rmd and .Rmd as markdown file types via Obsidian's registerExtensions API. This means Obsidian's native markdown editor and renderer handle the files — the plugin simply teaches Obsidian to recognize the extension.

On top of that, a markdown post-processor enhances the reading view:

• R code chunks (fenced with {r chunk-name, echo=FALSE}) get a visual header showing the engine, name, and options
• Inline R code (`r expression`) gets a small badge to distinguish it from regular inline code

Important: This plugin does not execute R code. It is a reader/display tool. To run R code, use RStudio, VS Code with R extension, or another R environment.

RMarkdown Syntax Support

Feature	Supported	Notes
YAML frontmatter	Yes	Rendered via Obsidian's built-in properties
R code chunks	Yes	Visual header with engine, name, options
Python/SQL/other engine chunks	Yes	Engine auto-detected from {engine} syntax
Inline R code	Yes	Badge display in reading view
Standard markdown	Yes	Handled by Obsidian natively
LaTeX math ($...$, $$...$$)	Yes	Handled by Obsidian natively
R code execution	Via command	Use the "Render document" command to run rmarkdown::render().

Known Limitations

LaTeX-style backtick-apostrophe quotes

Some RMarkdown/Pandoc users write quoted words using the LaTeX convention:

The policy was `agnostic' about the outcome.

Pandoc handles this via its smart-quotes extension, converting `foo' to proper curly quotes before parsing. Obsidian's markdown parser does not apply this transformation, so the opening backtick is interpreted as the start of an inline code span — which only closes when another backtick appears, sometimes far later in the document. The result is a large stretch of text rendered as code.

Workarounds:

• Use regular ASCII quotes: 'agnostic' or "agnostic"
• Use typographic curly quotes directly

This is a limitation of Obsidian's markdown parser, not the plugin. A future version may add optional Pandoc-style smart-quote preprocessing.

Commands

The "Create new RMarkdown document" command is always available. The other four require an .rmd/.Rmd file to be active in the editor.

Command	What it does
Open in RStudio	Launches RStudio with the current file.
Render document	Runs rmarkdown::render() via Rscript, then opens the generated output (HTML/PDF/etc.).
Reveal .Rproj in Finder/Explorer	Walks up from the current file to find the nearest .Rproj file and reveals it in your OS file manager.
Copy R chunks to clipboard	Extracts all R code chunks verbatim (preserving the ```{r …} fences) and copies to clipboard.
Create new RMarkdown document	Creates a new .rmd file seeded with RStudio's default html_document template and opens it. Placed in the active file's folder (or vault root), named Untitled.rmd with numeric suffixes for collisions.

Requirements

• Desktop only. Commands that launch RStudio or run R (Render document) use Node child_process and Electron APIs, which Obsidian exposes only on desktop. The plugin is marked isDesktopOnly accordingly.
• For Open in RStudio: RStudio must be installed. On macOS, the plugin uses open -a RStudio; on Linux/Windows, rstudio must be on your system PATH.
• For Render document: R and the rmarkdown package must be installed. Rscript and pandoc must be locatable by the plugin. The plugin probes common install locations so you usually don't need to do anything extra: on macOS it checks /usr/local/bin, /opt/homebrew/bin, and RStudio's app bundle; on Windows it checks standard Program Files locations for RStudio's bundled pandoc and the standalone Pandoc installer. If your setup differs, ensure Rscript and pandoc are on the PATH Obsidian inherits. The Windows R installer has an optional "Add to PATH" checkbox that is off by default — tick it during install, or add C:\Program Files\R\R-<version>\bin to your PATH manually.

Render errors

The Render document command runs your .rmd through rmarkdown::render() exactly as RStudio would. If the render fails, you will see a Notice showing the exit code (e.g. "Render failed (exit 1)") and the full R stderr will be logged to Obsidian's developer console (Cmd+Opt+I on macOS, Ctrl+Shift+I on Linux/Windows).

Common causes are not plugin bugs — they're R-side issues. The plugin will not auto-install anything for you. The render halts on whatever R or knitr encounters first:

• Missing R package: Error in library(foo) : there is no package called 'foo'. Fix by running install.packages("foo") in R.
• Missing Python for {python} chunks: the reticulate package must be installed and a working Python interpreter must be available to it. If reticulate's auto-install of Python fails (cache cleanup, sandboxing, etc.), set RETICULATE_PYTHON to an existing interpreter or call reticulate::use_python() in a setup chunk.
• Missing SQL driver or connection object for {sql} chunks: provide a connection=<DBI connection> chunk option against a pre-opened connection.
• LaTeX/TinyTeX not installed if rendering to PDF: tinytex::install_tinytex() in R.
• System-library dependencies (e.g. GDAL for sf, a JDK for rJava) must be installed at the OS level separately from R packages.

Any uninstalled R package or missing language runtime (Python, SQL driver, LaTeX) that one of your chunks references will cause the render to exit with a non-zero code. Check the console stderr for the exact line that failed and the fix will almost always be an install.packages(...) call or a system-level install — not a change to this plugin.

Development

# Install dependencies
npm install

# Run tests
npm test

# Dev build (watch mode)
npm run dev

# Production build
npm run build

License

MIT