There are a lot of additional features and tools of OTTR that are discussed here!

Citing sources

You can generally follow the Bookdown instructions about citations, but you don’t need to add the additional bibliography argument at the top of the Rmds.

To add a new reference source, add to the book.bib file, keeping your new entry in alphabetical order.

For articles (or anything with a DOI), go to doi2bib.org or ZoteroBib to get a BibTex-formatted reference that you can copy and paste the reference to the book.bib file.

You can also use programs like Zotero or Endnote to export a .bib file and either combine with the book.bib or manage your references from there.

Other sources can be added using this template:

@website{citekey,
    author = {First Last},
    title = {Title},
    url  = {www.website.com},
}

To reference the citations in your writing follow the bookdown instructions:

Items can be cited directly within the documentation using the syntax @key where key is the citation key in the first line of the entry, e.g., @R-base. To put citations in parentheses, use [@key]. To cite multiple entries, separate the keys by semicolons, e.g., [@key-1; @key-2; @key-3]. To suppress the mention of the author, add a minus sign before @, e.g., [-@R-base].

See Chapter 2 of this template course for examples.

This will automatically list references at the bottom of each chapter included in your course, as well as at the end of your course. Thus it is important to keep the References.Rmd file and to keep this as the last part of the _bookdown.yml file as it is in the template, so that this full list of references will be listed in a place that makes sense.

_bookdown.yml file showing the references file as the last file

Alternatively, you can add a header for this list of references as the last header in any other Rmd file that is listed as the final file of the _bookdown.yml file.

Giving credits to contributors

Since so many individuals contribute to our courses in so many ways. Thus, we decided to make a table of credits to make it clear who did what.

Here is an example:

Credit section from a course that used this template

Please see the about section of the template for descriptions of how credits should be attributed for the course.

This is generated from the About.Rmd file. An About.Rmd file will already be in your course from using our template. You will need to do the following steps to update it for your course:

  1. Fill out author names for the various roles where applicable.
  2. Delete lines for roles that are not applicable.
  3. Make sure roles grammatically match names. If there are multiple people include the “s” in the role name where applicable and remove the parentheses. If only one person is appropriate for a given role remove “(s)” from the role name.
  4. Ensure that each row has “|” around each cell value.

Example Table:

The first row and additional rows based on this table should be added and filled in using markdown table format.

|Credits|Names|
|-------|-----|
|Lead Content Instructor|FirstName LastName|

Links to personal websites can be added below the table to make it easier to read.

|Credits|Names|
|-------|-----|
|Lead Content Instructor|[FirstName LastName]|

<!-- Author information -->

[FirstName LastName]: link to personal website

These rows should be included for all courses:

|Template Publishing Engineers|[Candace Savonen], [Carrie Wright]|
|Publishing Maintenance Engineer|[Candace Savonen]|
|Technical Publishing Stylists|[Carrie Wright], [Candace Savonen]|
|Package Developers[ottrpal]|[John Muschelli], [Candace Savonen], [Carrie Wright]|

<!-- Author information -->

[John Muschelli]: https://johnmuschelli.com/
[Candace Savonen]: https://www.cansavvy.com/
[Carrie Wright]: https://carriewright11.github.io/

<!-- Links -->

[ottrpal]: https://github.com/jhudsl/ottrpal

These rows should be added to all Johns Hopkins courses:

|Content Publisher|[Ira Gooding]|
|Content Publishing Reviewer|Ira Gooding]|

<!-- Author information -->

[Ira Gooding]: https://publichealth.jhu.edu/faculty/4130/ira-gooding

Additionally, this row should be added for all ITCR Courses:

|Content Directors|[Jeff Leek]|

<!-- Author information -->

[Jeff Leek]: https://jtleek.com/

Adding the Credits table to Coursera

In Coursera, you can add the credits table URL as an ungraded plugin (the same as described here for adding chapter content). This should be added at the beginning of your course, right after the introduction.

Adding the Credits table to Leanpub

In Leanpub, make sure that your About.md file in your manuscript folder is listed in your Book.txt file and this Credits table will automatically be incorporated into your Leanpub course.

Borrowing chapters

If you have two courses that the content and topics overlap, you may want to share written material between the two.

But, if you copy and paste to share material this would create a maintenance problem because if you update one you will need to remember to copy over the other! 😱

In OTTR, we try to minimize maintenance pains so to get around this, we use cow::borrow_chapter() from the jhudsl/cow package. The cow package is already on the jhudsl/course_template docker image so you do not need to install it if you are using the docker image or if you are have GitHub actions do all the rendering for you.

To borrow a chapter from another course, create an .Rmd as you normally would, with a ottrpal::set_knitr_image_path() in a chunk at the beginning of the file and a H1 title.

Then, wherever you would like the borrowed chapter to appear, put an R chunk with this; where {r, echo = FALSE, results='asis'} is included in your chunk arguments.

cow::borrow_chapter(
  doc_path = "02-chapter_of_course.Rmd",
  repo_name = "jhudsl/OTTR_Template"
)

The magic of this function is that whenever the course is re-rendered it will knit the latest version of the chapter you are borrowing. Note that this chunk cannot be run interactively, just include it in your Rmd and render your course as usual.

Borrowing from a local file

If for some reason you would like a local file incorporated, just leave off the repo_name argument and cow::borrow_chapter() will look for the chapter locally: Have your chunk arguments include: {r, echo = FALSE, results='asis'}.

cow::borrow_chapter(
  doc_path = "02-chapter_of_course.Rmd"
)

Borrowing from a private repository

If you are borrowing from a course in a private repository, you will need to supply GitHub personal access token using a git_pat argument like this: Have your chunk arguments include:{r, echo = FALSE, results='asis'}

cow::borrow_chapter(
  doc_path = "02-chapter_of_course.Rmd",
  repo_name = "jhudsl/Private_Repo",
  git_pat = "12345"
)

Removing an h1 header

If you want to change the title you can use an option remove_h1 to remove the title from the incoming borrowed chapter.

Linking between chapters

If you don’t want the material from another chapter completely copied over, you might instead just want to put a link to the Bookdown chapter. You can just use the full url. A link would look something like this:

![](https://jhudatascience.org/OTTR_Template/a-new-chapter.html)

You might want your course available for download as a docx. For example, you might be running a “train-the-trainer” workshop where trainees don’t feel comfortable using Github to edit the lessons for their own use.

The following yml in index.Rmd allows you to render the docx with a table of contents:

output:
    bookdown::word_document2:
      toc: true

You can also incorporate a template docx if you have headers and logos you want to use. To incorporate a template, make sure you add the reference_docx argument:

output:
    bookdown::word_document2:
      reference_docx: <path/to/template>.docx
      toc: true

Learn more about templates here.

Compatibility with Google Docs

Google Docs can be a great way to get feedback from collaborators who aren’t comfortable developing in the GitHub environment. docx versions of the course are automatically rendered in pull requests and can be downloaded from the autogenerated comment.

  • Once you’ve downloaded the docx, this can be uploaded to Google Drive and shared with the individuals you would like to solicit feedback or new material from. In Google Drive, click + New in the left corner and then File Upload. Choose the docx file you downloaded.
  • You may also want to include a link to the commit ID the Google Doc came from so you are able to keep track of what changes have occurred since the Google doc was set up initially.
  • So you are able to keep track of the changes to the docx version of the course, its advisable to set to “suggestions” when you share the document.
  • Then as comments and suggestions trickle in, a lead author who is comfortable with the OTTR process can incorporate those comments into an existing or new pull request which can checked for its rendering and eventually added to the main content branch.