babette: first draft blog post #415

richelbilderbeek · 2019-01-25T14:41:58Z

As agreed with @stefaniebutland here, I submit the first draft of my babette blog post, as part of the rOpenSci onboarding process.

stefaniebutland · 2019-01-25T18:13:48Z

Thank you @richelbilderbeek.
This link shows the preview of your post: https://deploy-preview-415--ropensci.netlify.com/blog/2019/01/06/babette/

I have a couple of structural suggestions based on my first look. I can review the content on Monday Jan 28.

Thank you for acknowledging the reviewers. It's also very nice that you thanked people who supplied use cases and bug reports. Would you please link to them, e.g. GitHub or Twitter?
- I'd like to suggest an alternative wording for citing Guangchuang Yu's contribution: "Reviews were provided by David Wright and Joëlle Barido-Sottani, with a contribution from Guangchuang Yu."
- you might consider linking to the actual review thread as [text to link from](https://github.com/ropensci/software-review/issues/209), but that is optional
- Soon we will be specifically encouraging people to submit use cases in our discussion forum in a templated format, so it will be great to have those included. I'll follow up when your post is published
Please include only the images and blog post content themselves, but not e.g. themes/ropensci/static/img/blog-images/2019-01-06-babette/create_figures.R. You could include a link in the post to this content in your own repo if you would like to provide that. This might also apply to the xml file, but I have not yet checked the post details to see how it is integrated. Usually you would submit only .md and any image files.
add ! in front of each [](img/blog-images/2019-01-06-babette/phylogeny.png) to link to image
For references, in text, use [^1] and at bottom of post, use [^1]: blah blah reference
Example: https://ropensci.org/blog/2019/01/22/waterinfo-tidal-eel/#fn:1
Raw .md: https://raw.githubusercontent.com/ropensci/roweb2/master/content/blog/2019-01-22-waterinfo-tidal-eel.md. Link from DOI to the paper
tag software-peer-review -> Software Peer Review and r -> R
- very recent format change
Please create an author's index file for yourself as described here. This is a new feature in our site.

Please let me know if you would like me to clarify anything.

stefaniebutland

@richelbilderbeek This is a well laid out post that should be easy to understand for a reader not familiar with the subject area. I really like how you laid out the problem in the introduction. The "why rOpenSci" section gives a nicely written analogy between academic paper reviews and software review.

I have now reviewed the content and where possible, added suggestions in GitHub's "suggested change" feature that allows you to directly commit the suggested change if you agree with it.

Please tag me when you have addressed my suggestions here as well as the technical comments I made earlier and I will have another look before we publish.

Thank you!!

content/blog/2019-01-06-babette.md

Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com>

richelbilderbeek · 2019-01-29T06:24:42Z

Thanks for the feedback! And the fun experience to use GitHub review! I will process the feedback on Friday before 18:00 (Amsterdam time zone, UTC +1:00).

@stefaniebutland: what is the preferred order: getting the package CRAN first, or having a blog post first? (babette is not yet on CRAN)

stefaniebutland · 2019-01-30T01:36:54Z

what is the preferred order: getting the package CRAN first, or having a blog post first? (babette is not yet on CRAN)

That is your choice. If you're anxious to get it published, we could publish 2019-02-05. If you would like to wait until it's on CRAN, then we can keep the post as a pull request and only then set a publication date.

I will process the feedback on Friday before 18:00 (Amsterdam time zone, UTC +1:00)

Once that's done, I will set a time to review the updates. Thank you

Update fork

richelbilderbeek · 2020-01-15T13:32:44Z

@stefaniebutland: I've checked the R code and everything is still valid. Here the thumbs up 👍

stefaniebutland · 2020-01-17T00:49:49Z

@richelbilderbeek I will review the post for content by end of day Mon Jan 20.

stefaniebutland

Congratulations @richelbilderbeek. Looks like your post will be published almost exactly one year after your draft submission 😄 🎂

It's been a pleasure to read this again. I have made most of my comments inline in ...babette.md file. You are welcome to disagree with the subjective comments.

Preview of your post: https://deploy-preview-415--ropensci.netlify.com/blog/2019/01/06/babette/

Please change filename to 2020-01-28-babette.md and update the folder name and paths to images to use the new date

Thank you for your perseverance!

content/blog/2019-01-06-babette.md

stefaniebutland · 2020-01-21T03:15:19Z

content/blog/2019-01-06-babette.md

+package_version: 2.0
+authors:
+  - Richèl J.C. Bilderbeek
+date: 2019-01-06


Suggested change

date: 2019-01-06

date: 2020-01-28

set publication date (happy anniversary!)

Updated again to today.

stefaniebutland · 2020-01-21T03:28:09Z

content/blog/2019-01-06-babette.md

+are phylogenies. For example, this a phylogeny, with four species,
+eloquently named '1', '2', '3' and '4':
+
+![A phylogeny with four species](img/blog-images/2019-01-06-babette/phylogeny.png)


We now recommend using Hugo shortcodes to add images.

Example to be modified: {{< figure src = "/img/blog-images/2019-06-04-post-filename/name-of-image.png" width = "200" alt = "this is alternative text that describes the image" >}}

We now recommend that every image be accompanied by alternative text (alt="some 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. For information on what should go in alternative text, refer to this tutorial.

Updated all images 👍

stefaniebutland · 2020-01-21T03:41:56Z

content/blog/2019-01-06-babette.md

+
+### References
+
+[^1]: Bilderbeek, Richel JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). [doi.org/10.1111/2041-210X.13032](https://doi.org/10.1111/2041-210X.13032)


In preview (https://deploy-preview-415--ropensci.netlify.com/blog/2019/01/06/babette/#fn:1), looks like 1111/2041- in DOI is interpreted as math. Can you fix by escaping the /?

content/blog/2019-01-06-babette.md

Co-Authored-By: Stefanie Butland <stefaniebutland@gmail.com>

richelbilderbeek

Hi @stefaniebutland,

Thanks for the feedback! I accepted all of your suggestions, hoping I did not miss any.

I have not taken a look at the preview yet: gotta dash now, but can process any feedback tomorrow if needed.

Thanks 👍

richelbilderbeek · 2020-01-23T13:11:44Z

OK, most layout changes work nice on https://deploy-preview-415--ropensci.netlify.com/blog/2020/01/22/babette/. Will fix reference weirdness (see below) now.

…uation

richelbilderbeek · 2020-01-23T13:53:56Z

Hi @stefaniebutland, I processed all your feedback and am ready for more, if any 👍

stefaniebutland · 2020-01-23T21:23:49Z

Thank you @richelbilderbeek.

I made a few final fixes, but they can be found in this new pull request. (Sorry, I meant to add them to yours but I was trying something new to me.)

changes:

YAML date: 2020-01-28 gets set to publication date, not current date
renamed blog-images folder to 2020-01-28-babette and set paths in post to this folder
adjusted width in width = "200" to suit each image
added tag babette

I'll ask my colleagues for advice on fixing the reference formatting so it can be an active link. I'll fix it when I get a solution.

No more edits needed on your end. I'll note here when the ref formatting is fixed. Thank you for your work on this. I will publish and tweet on Jan 28.

richelbilderbeek · 2020-01-24T11:35:56Z

@stefaniebutland: thanks you some much, also for having the same perseverance 👍

I look forward to our next rOpenSci blog post 🌈

maelle · 2020-01-24T12:43:02Z

I'm very glad to be able to read this post since I'm handling the mcbette submission :-)

maelle · 2020-01-25T14:26:29Z

A few non-asked for remarks whilst I'm installing all mcbette dependencies 😉

In the blog post, I couldn't find a link to

the software review thread submission: babette ropensci/software-review#209
the official website https://docs.ropensci.org/babette/ (ICYMI @richelbilderbeek , see https://ropensci.org/technotes/2019/06/07/ropensci-docs/)

Would it make sense to mention you've submitted a further package for peer-review, and also whether you're intending to add even more R packages to the stack?

stefaniebutland · 2020-01-27T02:24:46Z

Addressed 2 of @maelle's comments in the other pull request #599 (comment)

maelle · 2020-01-27T05:17:22Z

I was a lazy reader hoping to be able to click from a single place 😂

richelbilderbeek · 2020-01-27T14:14:15Z

@maelle: sorry for the slower response. Everything is OK now? If no, let me know 👍

maelle · 2020-01-27T14:20:45Z

The point that's not in @stefaniebutland's corrected version of your post is "Would it make sense to mention you've submitted a further package for peer-review, and also whether you're intending to add even more R packages to the stack?" (but it's just a suggestion!).

maelle · 2020-01-27T14:21:15Z

(besides, I don't think the answer was slow, and I was aware I was posting on a week-end!)

@stefaniebutland

* Start babette blog post * EOD * EOD * EOD * babette: create nice figures * babette: progress * babette: first draft * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Commit suggestion Stefanie * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Process feedback #415 (comment) * Remove script and text files * babette: process feedback @stefaniebutland * add @richelbilderbeek author file * babette: progress blog post, progress ropensci/babette#56 * Add reference to babette article * Add reference to babette article * Mention GitHub usernames * Process feedback Stefanie, fix ropensci/babette#56 * Add dash before url * No URL in author field * Use form of monkeydo * End URL with slash * Align dashes * Remove URL * Only name in Authors field * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: richelbilderbeek <richelbilderbeek@users.noreply.github.com> * It's the thought that counts @stefaniebutland * It's the thought that counts @noamross * Add feedback @stefaniebutland, thanks! * Update content/blog/2019-01-06-babette.md Co-Authored-By: Stefanie Butland <stefaniebutland@gmail.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: Stefanie Butland <stefaniebutland@gmail.com> * Update content/blog/2019-01-06-babette.md Co-Authored-By: Stefanie Butland <stefaniebutland@gmail.com> * Process more feedback * Process more feedback * Process more feedback * Renamed '2019-01-06-babette.md' to '2020-01-28-babette.md' * Escape minus sign * Put link in code tags, as layout incorrectly thinks the link is an equation * Stef's edits * address Maelle's comments * rm ozunconf file added by accident * fix doi formatting * add ref as <https://doi.org/10.1111/2041-210X.13032> Co-authored-by: Richel Bilderbeek <richelbilderbeek@users.noreply.github.com>

richelbilderbeek · 2020-01-28T18:37:48Z

Uh, AFAICS the post is online. Would it still make sense to refer to my next package?

If yes: will fix tomorrow/Wednesdat
If no: sorry for being slow

stefaniebutland · 2020-01-28T18:48:55Z

Post is published: https://ropensci.org/blog/2020/01/28/babette/ and tweeted https://twitter.com/rOpenSci/status/1222190847900274688

I think it's ok to leave as is, but am happy to make the edit if you want to provide text. I'll close this PR once you confirm your decision @richelbilderbeek

No need to apologize for timing. You have been very prompt in submission and revisions.

richelbilderbeek · 2020-01-30T06:00:38Z

@stefaniebutland: Thanks, you did the right thing 👍

It was great working with you, thanks so much!

richelbilderbeek added 7 commits January 6, 2019 18:20

Start babette blog post

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EOD

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EOD

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babette: create nice figures

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babette: progress

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babette: first draft

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richelbilderbeek mentioned this pull request Jan 25, 2019

submission: babette ropensci/software-review#209

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Commit suggestion Stefanie

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Friday: process feedback blog post ropensci/babette#56

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babette: first draft blog post #415

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		### References

		[^1]: Bilderbeek, Richel JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). [doi.org/10.1111/2041-210X.13032](https://doi.org/10.1111/2041-210X.13032)

babette: first draft blog post #415

babette: first draft blog post #415

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