HTTPS SSH

hutchtemplates

This R package provides ready-to-use HTML output formats and templates for RMarkdown documents. The goal is to produce clean documents "out of the box", with or without the RStudio IDE. This package provides templates that are tailored for Fred Hutch.

This package is forked from rmdformats R package and currently only adds minor tweaks. See the original package for full details and implementations for a variety of templates.

The package provides several HTML output formats.

hutchthedown format

Format taken from the rmdformats::readthedown. Originally adapted from the corresponding readtheorg theme of the org-html-themes project, fully responsive with dynamic table of contents and collapsible navigation.

Features and helpers

Some extra features are available depending on the format :

  • hutchthedown is fully responsive, with collapsible navigation

The package also provides a create.doc() function as well as RStudio document templates to easily generate an empty and ready to use rmarkdown file with several configuration directives.

Finally, it also provides the pilltabs() helper function, which allows to display a crosstab dynamically.

Installation

install.packages(devtools)  # if necessary
devtools::install_bitbucket("robert_amezquita/hutchtemplates")

Creating a new document

Within RStudio

Choose File > New File... > R Markdown..., then select From Template. You should then be able to create a new document from one of the package templates.

Without RStudio

The create.doc() function allows you to create a new directory with a clean ready-to-use RMarkdown file. create.doc() gets two main arguments :

  • dirname is the name of the folder and RMarkdown file to be created
  • format is the format name ("html_clean" or "html_docco")

By default, a Makefile file will be created in the new folder for direct rendering from the command line.

Rendering

With RStudio

Rendering from within RStudio should be quite simple : just click the Knit button.

Rendering from R

You can render your document into HTML directly from within R with the render() function from the rmarkdown package :

library(rmarkdown)
render("mydocument.Rmd")

Rendering with the Makefile

If you created your .Rmd file with the create.doc() function, you can then generate HTML or PDF files with :

make html
make pdf

You can also clean out any generated files and cache with :

make clean

Credits

  • Magnific popup lightbox plugin
  • The code of create.doc() is heavily inspired by the create.project() function of the ProjectTemplate package
  • The CSS and JavaScript for readthedown is adapted from the corresponding readtheorg theme of the org-html-themes project, which is itself inspired by the Read the docs Sphinx theme.
  • JavaScript and HTML code for code folding and tabbed sections are taken from the RStudio's default rmarkdown HTML template