ADC Training Site

Practical open science approaches to Arctic research and data management

Acknowledgements

Work on this package was supported by:

• NSF award #1546024 to M. B. Jones, S. Baker-Yeboah, A. Budden, J. Dozier, and M. Schildhauer

Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.

About this repository

This repository is an integration of Blogdown and Bookdown. Some amount of wrangling was required to get all of this set up and not everything may be obvious to all viewers.

Helpful hints:

• Only check in your .Rmd files in the ./materials folder. Another service (Travis CI) does the rendering
• Live-preview your work bookdown::serve_book while you work
• Your changes will take a minute or two to appear on the website (because the site is built on a remote service)
• If the Travis CI build fails for your commit (see badge at top of readme) the site won't be updated (so fix the build)

How this works

Not everything is integrated nicely together so there are some folder organization conventions that need to be maintained for things to work. Changes to these conventions will require updating multiple pieces and will be error-prone.

• The root of the repository is a pretty standard Blogdown (See: Hugo) site.

• It's served using GitHub Pages but Travis CI does the task of pushing the prepared site content from the master to gh-pages branch.

  The reasonfor this is because each course's material are a Bookdown book and Blogdown doesn't know how to render Bookdown books and we wanted Travis CI to build everything so we could ensure our own work was reproducible

• A root-level DESCRIPTION file is present to trick Travis CI into running

• Bookdown books are stored in /materials as subfolders within

• The books are built on Travis CI and moved into the site's public directory by Travis CI running ./build_and_merge.sh during the job.

Adding a new Event

Add a new subfolder at ./content/events/{your-training-name}, replacing {your-training-name} with a short title for the training and write up an index.md in that folder with your content. I'd suggest just copying an existing event and modifying it for your needs.

Adding a new Book (Material)

• Add a new Bookdown book into ./materials/. I'd suggest copying an existing book and modifying it to your needs. Make sure the DESCRIPTION file in the root of your book (not the root of this repo) contains the necessary Imports to load all of the packages required by your book. Travis CI installs each book's dependencies just prior to building the book by running devtools::install_deps('.') in the book's top level directory.
• Manually add a link in ./content/materials.md

Working on a Book (Material)

To work on a Book (e.g., edit a chapter), you will want to do a couple of things to get properly set up. Each Book is in its own sub-folder of ./materials. and should have its own .Rproj file inside its particular subdirectory.

If you haven't already cloned this repository, you'll want to do that:

git clone https://github.com/nceas/sasap-training

Once that's done, cd into the subfolder within ./materials for the Book you want to edit and open the .RProj file:

# Just an example:
cd sasap-training/materials/reproducible-analysis-in-r/
open reproduceible-analaysis-in-r.Rproj

If you system is set up like mine is, RStudio should open. While working on whatever chapter(s) you want to work on, you may want to preview them before committing your changes. You can use the Knit button in RStudio, but it's maybe even nice to use Bookdown's live-reloading functionality:

bookdown::serve_book(".")

As you edit and save your work, the Viewer Pane in RStudio should automatically update with your rendered changes.