3  Technical Guidelines

This chapter explains the technical details of submitting a blog post or tech note (referred to collectively as “posts”) for publication on the rOpenSci website - from drafting in an (R) Markdown template, to submitting for review using GitHub Pull Request infrastructure.

We include advice on commonly used elements like adding an image, a citation, or embedding a tweet in case you need them.

Briefly, the process is:

  1. Get the go-ahead and a tentative publication date from our Community Manager.
  2. Fork the repository (repo) of the rOpenSci website.
  3. Draft your post in R Markdown or Markdown and create or update your author metadata.
  4. Preview and refine your post locally.
  5. Submit via pull request and preview your post.
  6. A blog editor reviews your post.
  7. Revise your post in response to review.

This chapter links to templates for posts and checklists that you can also find in the Appendix.

3.1 Fork the roweb3 repository

Fork the rOpenSci website repository and create a new branch to work on your post. For help with this aspect of git/GitHub, we recommend happygitwithr and the pull request helpers of the usethis package.

3.2 Install blogdown

If you plan to use R Markdown to write your post (using index.Rmd as opposed to directly writing it in Markdown with index.md and not executing any code), please install or update blogdown.

install.packages("blogdown")

3.3 Author files

Create or update your author file.

3.3.1 Why?

The rOpenSci website has a page listing all authors who have contributed to a blog post, tech note, or presented in a Community Call. A click on your by-line in a post takes the reader to your author page that has links to your online home, possibly your Twitter or GitHub profile(s), and a list of all the content you’ve authored on our site. For staff and leadership team members, editors for software peer review, or members of our Code of Conduct Committee, their rOpenSci title is also listed on their author page.

3.3.2 How?

If you don’t already have an author page, create a folder called yourfirstname-yourlastname in your local copy of roweb3/content/author/. You can have accents, middle initials, or hyphens appear in your name if you name your folder appropriately. That can be tricky so we have examples below.

In that folder, create a file called _index.md with information about your online presence. You can copy this template below (or get it via roblog after installing it via install.packages("roblog", repos = "https://dev.ropensci.org") ).

author-file-template.md

---
name: {author_name}
link: website URL or other online presence
twitter: Twitter username
github: {github_username}
gitlab: GitLab username
keybase: Keybase ID
orcid: {orcid_id}
---


At minimum, provide your name and a link or your Twitter, GitHub, or GitLab username. Add your usernames or ID’s without the “@” or the “https:…”. The link field can be your personal website URL, for example.

3.3.3 Examples

This author file, /author/kelly-obriant/_index.md

---
name: Kelly O'Briant
link: https://kellobri.github.io/
twitter: kellrstats
github: kellobri
---

… generates Kelly O’Briant’s author page

Screenshot of Kelly O'Briant's author page

This author file, /author/maëlle-salmon/_index.md

---
name: Maëlle Salmon
twitter: ma_salmon
bio: rOpenSci Research Software Engineer, Associate editor of rOpenSci Software Peer Review
github: maelle
gitlab: maelle
keybase: maelle_salmon
orcid: 0000-0002-2815-0399
---

… generates Maëlle Salmon’s author page.

For an example of how to name the folder with an accent and initials, see this author file that generates Richèl J.C. Bilderbeek’s author page. The folder name must include accents, initials with periods, and hyphens for spaces, in order to link to their blog content.

Look at other people’s folder names for examples.

3.4 Post template

Start your post from a template. If you use RStudio, refer to the instructions to create your draft with blogdown’s New Post Addin. If not, refer to the instructions to create your draft manually.

3.4.1 New Post Addin

The blogdown New Post RStudio addin creates the post draft in the correct location and fills the post YAML based on metadata you’ll have entered.1

  • Install whoami and blogdown (install.packages(c("whoami", "blogdown"))) (blogdown version should be at least 1.6.0).
  • Install Hugo (to preview the post): blogdown::install_hugo("0.89.0") (version recorded in netlify.toml of the roweb3 repository).
  • Re-start R.
  • In RStudio, open the forked roweb3 project.
  • Create a new post by running Addins > New Post or blogdown:::new_post_addin().
  • Leave “Categories” blank (and ignore in the file created)

blogdown's New Post Addin.

  • Enter a title, no need to worry about title case at this stage.
  • Enter your name if whoami wasn’t able to guess it.
  • Choose the correct date.
  • Enter a new slug if the default one is too long.
  • Choose “blog” as a Subdirectory from the drop-down menu.
  • Choose an Archetype, Rmd or md, from the drop-down menu.
  • Also choose the correct Format: .Rmd if Rmd, Markdown (.md) if md. Never choose .RMarkdown.
  • Ignore Categories.
  • Select “tech notes” tag if this is a tech note
  • Select any other relevant tags and/or create new ones
  • Click on “Done”, your post draft will have been created and opened.

3.4.2 Manually

Create a folder YYYY-MM-DD-slug/ (e.g. 2020-01-20-rorcid/) under /content/blog/ Your post source and its images should live in /content/blog/YYYY-MM-DD-slug/.2

  • R Markdown template is to be saved as /content/blog/YYYY-MM-DD-slug/index.Rmd. It will need to be knit (RStudio knit button, or blogdown::build_site(build_rmd = <path_to_file>)). Add both index.Rmd and index.mdto your PR.

  • Markdown template is to be saved as /content/blog/YYYY-MM-DD-slug/index.md.

3.5 Adding content

3.5.1 YAML

The YAML sets the metadata for a post. This is the YAML from our post template, with comments to explain some components.

Note: The New Post Addin automatically creates a categories component, but you should ignore or remove this and use tags instead.

slug: post-template
title: Post Title in Title Case
package_version: 0.1.0
author:
- Author Name1
- Author Name2
date: '2020-03-10'
tags:
- Software Peer Review
- packages
- R
- community
description: A very short summary of your post (~ 100 characters)
twitterImg: blog/2019/06/04/post-template/name-of-image.png
twitterAlt: Alternative description of the image
tweet: A post about blabla by @username!

3.5.1.1 Subject tags

Add tags to the YAML of your post to make it more findable. Browse our page that lists all tags in use and re-use an existing tag rather than creating a new one e.g. ‘packages’ exists, so use that, rather than ‘package’.

For a post about your peer-reviewed package, use ‘Software Peer Review’, ‘community’, ‘packages’, the package name, and any others you see fit.

3.5.1.2 Twitter cards metadata (optional)

If you’re curious about the description, twitterImg, twitterAlt YAML fields in the post metadata and how they can help draw readers to your post, refer to our explanation of Twitter cards.

Delete description, twitterImg and twitterAlt YAML fields if you don’t use them.

3.5.1.3 Default Twitter text (optional)

Provide default text for tweets when a reader clicks the “Share on Twitter” button by replacing the value of tweet: "A post about blabla by @username!". Consider including your (and your coauthors) Twitter handle(s) (@username) in the tweet text to ensure you get notified when someone shares your post.

3.5.2 Images - General

Images can either be external or created in rmarkdown. Regardless of how images are included, they should all contain alt text and consider the following features.

Alt text
Every image should be accompanied by alternative text to make it more accessible to people with disabilities and provide a better user experience for everyone. The alternative text should convey the meaning or content that is displayed in the image. Refer to this tutorial for details on what should go in alternative text, and see the following sections for how to include alt text.

Image features

  • Consider transparent backgrounds as the blog background is not white (hex logos etc. will look better this way)
  • Keep images < 1 mb

3.5.3 Images - External

This section refers to images that are not generated from R Markdown. If you want to generate images from R Markdown use our R Markdown template and see next subsection.

File location
All images go in the same folder as your post source (/content/blog/YYYY-MM-DD-slug/) (do not link to external services like imgur). To reference them in your post, use name-of-image.png.

Insert an image

  • Insert an image with either figure or imgtxt short codes
    • Note the use of alt = to specify alt text
    • {{< figure src = "image-name.png" alt = "informative description" >}}
    • imgtxt:
{{< imgtxt src = "image-name.png" alt = "informative description">}} 
Text to right 
{{< /imgtxt >}}

Image placement

  • Basic positioning with {{< figure >}} and class

    {{< figure src = "image-name.png" alt = "informative description" class = "center" >}}

    • pull-left - Left-align the picture and wrap text around it
    • center - Center the picture (no text wrapping)
    • pull-right - Right-align the picture and wrap text around it

  • Specific text next to image with {{< imgtxt >}}

    {{< imgtxt src = "image-name.png">}} Text to right {{</ imgtxt >}} Text below

    • Only text between {{< imgtxt >}} and {{</ imgtxt >}} is to the right of the figure

  • For images side-by-side, create a composite and insert as a single image
    • Consider gimp for free and open source image manipulation software
    • Consider the R package patchwork for combining R figures

Other details

  • Control image size with width
    {{< figure src = "image-name.png" width = "400" alt = "informative description">}}

  • Make the image a hyperlink with link
    {{< figure src = "image-name.png" alt = "informative description" link = "http://hyperlink">}}

Important! In R Markdown (i.e. in *.Rmd files but NOT *.md files), these Hugo shortcodes need to be escaped:

<!--html_preserve-->
{{< figure src = "name-of-image.png" width = "400" alt = "informative description">}}
<!--/html_preserve-->

3.5.4 Images - Rmd-created

File location
When using our R Markdown template the knitr hook in the setup chunk actually creates the necessary Hugo shortcodes. Therefore you don’t need to worry about paths.

Image details
In the chunk producing a figure, use the hugoopts chunk option to control the alt text and other elements. hugoopts is a named list that can have all elements described in the documentation of the Hugo figure shortcode except for title.

```{r chunkname, hugoopts=list(alt="alternative text please make it informative", caption="this is what this image shows, write it here or in the paragraph after the image as you prefer", width=300)} 
plot(1:10)
```

This chunk above produces a figure with “alternative text please make it informative” as alternative text, “title of the image” as title, “this is what this image shows, write it here or in the paragraph after the image as you prefer” as caption, and a width of 300 pixels.

3.5.5 Citations and footnotes

To add citations, refer to them in the body of your post as footnotes:

Citation of the primary literature[^1].
Citation of an R package[^2].
Citation of a website[^3].

And list your sources at the bottom of your post:

[^1]: Sciaini, M., Fritsch, M., Scherer, C., & Simpkins, C. E. (2018). NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R. Methods in Ecology and Evolution, 9(11), 2240-2248. <https://doi.org/10.1111/2041-210X.13076>
[^2]: Elin Waring, Michael Quinn, Amelia McNamara, Eduardo Arino de la Rubia, Hao Zhu and Shannon Ellis (2019). skimr: Compact and Flexible Summaries of Data. R package version 2.0.2. https://CRAN.R-project.org/package=skimr
[^3]: Hugo static site generator. https://gohugo.io/

3.5.5.1 Finding citations

To get the citation for an R package, run citation("packagename").

To get the citation for an article, you can use the RStudio Addin for rcrossref, or get the citation from a paper’s DOI by running e.g.

rcrossref::cr_cn("10.1111/2041-210X.13076", format="text", style="apa")

[1] "Sciaini, M., Fritsch, M., Scherer, C., & Simpkins, C. E. (2018). NLMRandlandscapetools: An integrated environment for simulating and modifying neutral landscape models inR. Methods in Ecology and Evolution, 9(11), 2240–2248. doi:10.1111/2041-210x.13076"

To get the citation for an article in Google Scholar, find the article, click the quote symbol (in search results under the article) to open the “Cite” window, and copy the APA style text.

Get a citation from Google Scholar.

3.5.6 Embedded tweets

Use a Hugo shortcode to embed a tweet using its username and its ID e.g. {{< tweet user="SanDiegoZoo" id="1453110110599868418" >}}. In R Markdown, shortcodes need to be html escaped, refer to the template for an example.

If you want to quote a tweet and make it look more subdued, you can use a block quote linking the tweet. Example, source.

3.5.7 Block quotes

3.5.7.1 Block quotes with no attribution

E.g. if you want to highlight a sentence from the post itself.

Block quotes are paragraphs starting with >.

If you want to have them right-align add {.blockquote .text-right} right after the paragraph e.g.

> blabla
blabla
blabla
{.blockquote .text-right}

If you want to have them centered add {.blockquote .text-center} right after the paragraph e.g.

> blabla
blabla
blabla
{.blockquote .text-center}

3.5.7.2 Block quotes with attribution

If you want to add a block quote with an author name, use:

{{< quote footer="Author Name">}}
Blablablabla  
{{< /quote >}}

If you want to add a block quote with an author name and a source, use:

{{< quote footer="Author Name" cite="[good book](url)">}}
Blablablabla  
{{< /quote >}}

If you want to center the block quote add the align variable:

{{< quote footer="Author Name" cite="[good book](url)" align="center">}}
Blablablabla  
{{< /quote >}}

If you want to right-align the block quote add the align variable:

{{< quote footer="Author Name" cite="[good book](url)" align="right">}}
Blablablabla  
{{< /quote >}}

Note that this syntax also work for quotes without attribution!

{{< quote align="center">}}
Blablablabla  
{{< /quote >}}

3.5.8 Tables

If you want to use e.g. striped tables, add {.table .table-responsive .table-striped} right after the last line of the table.

Header   | Other Header | Another Header
---------|----------------|-------------------
Value 11 | Value 12       | Value 13
Value 21 | Value 22       | Value 23
Value 31 | Value 32       | Value 33
{.table .table-responsive .table-striped}

3.5.9 Examples

Comparing the raw Markdown to the live posts in these examples might be helpful.

3.6 Style Guide

  • For formatting of package names, functions, and code, follow the tidyverse style guidance. Format package names as regular text (no quotes).
  • Do not use markdown in titles (but you can use them in headings).
  • Use ## and ### to format headings in your post, i.e. section titles as ## (h2) and subsections as ### (h3), #### (h4).
  • Use title case for the title of your post; use sentence case for headings inside the post.
  • ‘rOpenSci’ not ‘ROpenSci’
  • When adding rOpenSci links to your post, use relative instead of absolute URLs e.g. /blog/ instead of https://ropensci.org/blog/.
  • When linking to rOpenSci packages use their docs.ropensci.org URL, e.g. https://docs.ropensci.org/drake/.
  • Use Hugo shortcodes (not html) to add images, tweets, gists etc.
  • In R Markdown wrap Hugo shortcodes between html preserve tags as shown in the template.
  • Instead of using html widgets (DT, leaflet, etc.), include a screenshot and use the link option of the Hugo figure shortcode to direct readers to an online version of the widget.
  • Use informative alternative text for all images.
  • Add new line at end of each sentence (makes diffs easier to interpret and easier for editor to suggest specific changes).

3.7 Pre-submission checks

3.7.1 Knit post

If using the R Markdown template, knitting index.Rmd (RStudio knit button, or blogdown::build_site(build_rmd = <path_to_file>)) will generate index.md. Commit both index.Rmd and index.md.

3.7.2 Check with roblog

You can use functions in the roblog package to do some automated checks on your post.

  • ro_lint_md() to check and enforce use of complete alternative descriptions for image, of relative links to rOpenSci website, of Hugo shortcodes for tweets.
  • ro_check_urls() to check for URLs that might be broken

3.7.3 Author Checklist

Pick the appropriate checklist for your post and ensure you checked everything off. Notice the copy-paste button at the top-right corner of the list.

3.7.3.1 Posts on peer-reviewed packages

* [ ] I have read the Content Guidelines.
* [ ] I have read the Technical Guidelines.
* [ ] I used or followed the R Markdown or Markdown template.
* [ ] I have followed the Style Guide.
* [ ] I created or updated my author metadata with correct folder name.
* [ ] I have added relevant tags after browsing existing tags (including "community" tag).
* [ ] I have added the "tech notes" tag if this is a technote.
* [ ] I ran `roblog::ro_lint_md()` on index.md (optional).
* [ ] I ran `roblog::ro_check_urls()` on index.md (optional).
* [ ] I ran a spell-check on index.md.
* [ ] I have added the tags - Software Peer Review, my-packagename.
* [ ] I have added the package-version YAML tag.
* [ ] I have added acknowledgement of the reviewers' work (with links to reviewers).
* [ ] I have added a link to the software peer review thread.

3.7.4 Local preview

If you wish to preview your post locally, as it will appear in our site, you must install Hugo. To install, refer to Hugo docs or run blogdown::install_hugo() using the version recorded in netlify.toml.

Note: You can also preview your blog post online through the pull request before the final submission.

Then run hugo serve or blogdown::serve_site() in the repo directory to start a local server on http://localhost:1313 (or another one indicated by blogdown).

Note: If you are used to using hugodown you can use it instead to serve the website.

The version of Hugo used by the rOpenSci web server is defined in netlify.toml.

When this preview looks good to you, you should submit your post as a pull request.

3.8 Submit draft post

3.8.1 Create draft pull request

  • Open a draft pull request (PR) from your fork (using the web interface, see step 8 for creating a draft), or usethis::pr_push() that will save you some work and that will in the end open the same web interface where you can choose Draft PR in the last step)

  • If you opened a PR instead of a draft PR, you can convert it to a draft by clicking on “Still in progress? Convert to draft” on the right panel under “Reviewers”.

3.8.2 Add checklist

In the first comment of your pull request submitting a post, please copy-paste the checklist corresponding to your post and check off the items.

3.8.3 Preview online

From the PR, Netlify will start building the new version of the site within seconds and you can preview your changes to make sure everything looks as intended. Otherwise push additional fixes till things look right.

Some checks haven't completed yet.

All checks have passed.

3.8.4 Submit post

  • Mark the draft PR as ready for review at least one week prior to the planned publication date. When you get approval for a post idea you’ll be told who to ping as your reviewer.

  1. If you don’t use RStudio you can still use the addin, but the new post will be opened in the editor returned by getOption("editor"), that you might need to configure.↩︎

  2. In Hugo speak, we’d say your post is a leaf bundle.↩︎