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This script builds on Aleszu Bajak's excellent [tutorial on building a course website using R Markdown and Github pages](http://www.storybench.org/convert-google-doc-rmarkdown-publish-github-pages/). It automates the rendering of HTML files from RMD and automatically generates the page menu for the site, eliminating much duplicative work.
# This script builds on Aleszu Bajak's excellent
# [tutorial on building a course website using R Markdown and Github pages](http://www.storybench.org/convert-google-doc-rmarkdown-publish-github-pages/).
# I was excited about the concept but wanted to automate a few of the production steps: namely generating the HTML files
# for the site from the RMD pages (which Aleszu describes doing one-by-one) and generating the site navigation menu,
# which Aleszu handcodes in the `_site.yml` file. This script should automate both processes, though it may have some quirks
# unique to my setup that you'd want to tweak to fit your own. It's likely more loquacious than necessary as well, so feel free
# to condense as you can. Ideally, each time you make updates to your RMD files you can run this script to generate updated HTML
# pages and a new `_site.yml`. Then commit changes to Github and you're up and running!
# Once you've got everything configured for your own site below, you should be able to run `source('renderSite.R')`
# in your console to generate updated HTML files and an updated menu. You could probably add some Github code to the
# very end to build the commit into the script.
#list all the RMD files in your site's directory
files <- list.files(path = ".", pattern = '*.Rmd', full.names = FALSE)
#this function runs over all the RMD files and renders them to their default output (hopeful HTML)
lapply(files, function(x) {
rmarkdown::render(paste0(x))
})
# here I set a few variables for the course that I can paste into the strings below
courseTitle <- "Your Course Title Here"
navTitle <- "Your Navigation Title Here"
profName <- "Your Name"
profEmail <- "Your Email Address"
# this generates a list of the HTML files created in lines 8-10
html_files <- list.files(path = ".", pattern = '*.html', full.names = FALSE)
# the code below works through the listed HTML files and generates a list of strings, formatted as required in the
# `_site.yml` file, that includes each of the site's pages and URLs. It generates the page name in upper case but you could
# tweak that as desired. This does name the pages based on their HTML filenames; if you wanted something more
# descriptive you'd have to write some more code here.
pages <- lapply(html_files, function(x) {
pageName <- sub('\\.html$', '', x)
paste0(' - text: \"',paste(toupper(substr(pageName, 1, 1)), substr(pageName, 2, nchar(pageName)), sep=""),'\"\n',
' href: ',pageName,'.html','\n')
})
# these collapse the list into a single string. This also renames the "Index" menu item as "Description."
# I put my course description in the `index.html` file so it's the first thing that loads with the site,
# but I think calling the page "Index" in the site menu would be confusing for students. If there were other pages you
# knew you'd want to rename consistently every time you generated the site, you could use the `sub` function to do so.
pages <- paste(pages, collapse = "")
pages <- sub("Index","Description", pages)
# this pastes the standard boilerplate from the top of the `_site.yml` file together with the list of pages
# generated above. This also adds a final menu item with a link to email the professor established in the variables above.
yml <- paste0('name: ',courseTitle,'\n',
'output_dir: \".\"','\n',
'navbar:','\n',
' title: \"',navTitle,'\"','\n',
' left:','\n',
pages,
' - text: \"Email Prof. ',profName,'\"\n',
' href: mailto:',profEmail)
# finally, this writes everything generated above into (what should be) a valid `_site.yml` file.
# Commit the folder to github and everything should be updated!
write(yml, file="_site.yml")

This is great. Playing around with it, I found that adding something like

output:
   html_document:
     toc: true
     toc_depth: 2
     toc_float: true
     theme: cosmo

to each Rmd file made for nice output.

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