Ocean Health Index Toolbox Training materials

These materials are available as a book at http://ohi-science.org/toolbox-training.

Please clone or download https://github.com/OHI-Science/toolbox-demo to accompany this training.

To render this book: bookdown::render_book("index.Rmd", "bookdown::gitbook")

Many thanks to the creators of bookdown:

• Yihui Xie (2016). bookdown: Authoring Books and Technical Documents with R Markdown. R package version 0.3.9.
• Yihui Xie (2016). bookdown: Authoring Books and Technical Documents with R Markdown. Chapman and Hall/CRC. ISBN 978-1138700109

Publishing with the /docs folder

Here is how to publish this book using the docs/ folder (instead of using Travis-CI or some script to move content between branches like we did with _deploy.r).

In RStudio:

1. In the root directory of your book, create a folder called docs (all lowercase)

2. In _bookdown.yml, add a line that says output_dir: "docs" (no indentation)

3. Check your .Rproj file (may have to open a separate text editor for this). Make sure that lines ~12 on say the following (replace whatever is there):

   RnwWeave: knitr
   LaTeX: pdfLaTeX
   
   AutoAppendNewline: Yes
   StripTrailingWhitespace: Yes
   
   BuildType: Website
   

4. Quit RStudio. When you reopen, your "Build" tab in the top right pane should have a button that says "Build Book"

5. Build your book by clicking the button or in the console: rmarkdown::render_site(encoding = 'UTF-8')

6. Delete the _book folder if it exists (this is what _deploy.R used)

7. Commit and push

On GitHub.com

1. Go to your repo > Settings
2. Scroll down to GitHub Pages
3. Change "Source" to "master branch /docs folder", click "save"
4. Delete the "gh-pages" branch, if it exists ("Branches" is next to "commits" on the "Code" tab)

Back in RStudio

1. Edit your book, rebuild, commit, and push and see the changes!