RMarkdown and websites

source: rstudio/rmarkdownwebsites.md

:link: Documentation on authoring webpages using RMarkdown and Github (to host the site)

:link: Other helpful resources

YAML

Example _site.yml doc

name: "Bioinformatics & Phylogenetics"
output_dir: "docs"
navbar:
  title: "Code"
  left:
  - text: "Home"
    href: index.html
  - text: "RStudio"
    icon: fa-file-alt
    menu:
      - text: Introduction
        href: rstudio-intro.html
      - text: "---------"
      - text: "Plots & data"
      - text: Aesthetics
        href: rstudio-aesthetics.html
      - text: Plots
        href: rstudio-plots.html
      - text: Statistics
        href: rstudio-statistics.html
      - text: "---------"
      - text: "RMarkdown"
      - text: Introduction
        href: rmd-intro.html
      - text: Bookdown
        href: rmd-bookdown.html
      - text: Websites
        href: rmd-webpages.html
  - text: "Sequence files"
    icon: fa-dna
    menu:
      - text: Command line
        href: sequence-files.html
      - text: Visualising and editing
        href: visualise.html
      - text: "Muscle"
        href: muscle.html
  - text: "Phylogenetics"
    icon: fa-code-branch
    menu:
      - text: "Introduction"
        href: phylo-intro.html
      - text: "Evolutionary models"
        href: evolutionary-models.html
      - text: "IQ-TREE"
        href: iqtree.html
      - text: "MrBayes"
        href: mrbayes.html
output:
  html_document:
    theme: yeti
    highlight: monochrome
    include:
      after_body: footer.html

Icons for webpages

A blog here

Font Awesome icons

Themes

If using the Simple R Markdown website option to create a website then the default available themes options include: "cerulean", "cosmo", "cyborg", "darkly", "flatly", "journal", "lumen", "paper", "readable", "sandstone", "simplex", "slate", "spacelab", "superhero", "united", "yeti"…check them out here. Highlight options include: "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", "haddock", "breezedark", "textmate".

Overiew here

They can be changed by including the following in the ‘YAML'

output:
  html_document:
    theme: united
    highlight: monochrome

Bootswatch

Library here

Bootstraplibs

remotes::install_github("rstudio/bootstraplib")
library(bootstraplib)

To start using bootstraplib in your rmarkdown::html_documents, install the following:

remotes::install_github("rstudio/rmarkdown#1706")

Use bootstrap_version and theme to choose the Bootstrap version and a Bootswatch theme. These arguments are currently supported only in html_document and html_document_base.

---
output:
  html_document:
    bootstrap_version: 4+3
    theme: minty
---

You can also add theme customizations inside any R code chunk (these customizations end up influencing the Bootstrap CSS included in the output document).

library(bootstraplib)
bs_theme_accent_colors(primary = 'green')

Some extra info here

Extra

Get extra bits of html from the bootswatch theme webpages. E.g. minty

Footers

You can add footers to your webpages. Add a footer.html file to your directory and insert the following.

 
<hr />
<p style="text-align: center;">Work by <a href="https://github.com/siobhon-egan">Siobhon Egan</a></p>
<p style="text-align: center;"><span style="color: #808080;"><em>siobhon.egan@murdoch.edu.au</em></span></p>

<!-- Add icon library -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">

<!-- Add font awesome icons -->
<p style="text-align: center;">
    <a href="https://siobhon-egan.github.io/" class="fas fa-home"></a>
    <a href="https://www.researchgate.net/profile/Siobhon_Egan" class="fab fa-researchgate"></a>
    <a href="https://github.com/siobhon-egan" class="fa fa-github"></a>
</p>

&nbsp;

Edit your YAML to include the following

output:
 html_document:
    theme: united
    include:
      after_body: footer.html

For a more simple footer, use the following

<p> <font size="2"><font color="purple">Copyright &copy; 2020 Siobhon Egan. </font></font> </p>

Bootstrap customisation

Further HTML customisation with the bootstrap theme available here

Blogdown

Another option of creating a website in RStudio is using Blogdown.

Useful resources and examples