R Markdown

These pages are in R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When in RStudio you click the Knit button and a document will be generated that includes both content as well as the output of any embedded R code chunks within the document.

For more information - contact

Notes on Website creation

Assuming R and RStudio are already installed and R Markdown is being used for files.

Steps

  1. Create Github account
  2. Create Github Repo (folder) and make it public
  3. Go to settings - Git Hub pages - Source - and make it “Master branch”
  4. Upload existing R files to Repo (include a _site.YML and index.rmd, see following pages)
  5. Create a .nojekyll file (to stop Github from trying to make a wesite)
  6. Create a index.html redirect in Repo master folder to redirect to _Site folder that RStudio is about to make (see following page re direct HTML)
  7. Download Git to computer
  8. In Git CMD (depreciated)
  9. git config –global user.email “”
  10. git config –global user.name “Your Name”
  11. In RStudio Go to tools global options and check it is pointing to the git.exe (mine is at C:/Program Files/Git/bin/git.exe)”
  12. View SSH RSA Key while there - copy to GitHub - your_user_ID - Edit Profile (at top of page not side) - Personal Settings - SSH and GPG Keys
  13. Back in Rstudio - open a new project with version control
  14. Provide the URL for Git Hub repo - this should make a new folder on your PC with the Git Hub Repo name and download all the files back to your PC
  15. Use Rstudio to Build the website
  16. I havent had much joy pushing the website to Github using Rstudio so
  17. After “Build” website in RStudio go back to the Windows Start Menu - Git CMD (Deprecated) to cd.. and cd into right directory then
git add -A
git commit -m “new website”
git push

And your new website should be up and running at
https://Github_user_name.github.io/Github_repo_name/_site/
ie for captif-nz https://captif-nz.github.io/LTPPNZ/_site/

And remember you need that redirect index.html in github repo
and a .nojekyll file made (with nothing actually in it)

Updating Website in RStudio

  • Pull first from the Git tab in RStudio
  • Make and save changes to RMD files then
  • Tick and commit in RStudio Git tab
  • Give commit a name and push from the commit box in Rstudio
  • Test the new look by “knitting”” the new page (except the index)
  • Build a new website if figures or pictures are on a updated page
  • If you dont need to build you can commit and push the html created
  • If pushing a new website, use step 17 above

Note.
- “Kniting” HTML isn’t the same as “Building” a website.
- Knitting includes pictures in the HTML, making it slow to load
- Building strips out the pictures and links to them - making it fast

index.html Redirect file

You will need a redirect file called index.html that gets loaded directly to the Githun master repo. This just makes the link to the _site folder the RStudio creates you website in.


<html>    
    
<head>    
    
<title>Redirecting to LTPP Data site  
</title>    
    
<meta http-equiv="refresh" content="1; URL=https://captif-nz.github.io/LTPPNZ/_site">    
    
<meta name="keywords" content="automatic redirection">    
    
</head>

index.Rmd

You will also need a file called index.RMD file to act as a home page (It can contain anything) when you build the website in Rstudio - if you use the _Site.yml file format on the next page. Unfortunately if you knit this file you will over write the index.html file for the repo-master folder from the previous page. And it must be called index as the github looks for index in the folder - tried calling it something else and wasn’t successful.

##_Site.yml file

You will need create a text file in R Studio called “_Site.yml” in the R Project that looks a bit like this below. It is the structure of your site. That index file is not the same as the one mentioned above as a redirect - this a RMD file called index that is built for the webiste as its home page

name: "LTPP-website"  
navbar:  
  title: "LTPP Website"  
  left:  
    - text: "Home"  
      href: index.html  
    - text: "About"  
      href: about.html  
    - text: "LTTP Summary"  
      href: LTTP-Summary.html  
    - text: "Rutting Summary"  
      href: Rutting-Summary.html  
    - text: "Roughness Summary"  
      href: RoughnessSummary.html  
    - text: "Texture Summary"  
      href: TextureSummary.html  
    - text: "Ratings Summary"  
      href: Ratings.html
    - text: "Table Summary"  
      href: Table-Summary.html