mcbette blog post

[richelbilderbeek]

Hi @steffilazerte,

Here I post my suggested version for an mcbette blog post with a deadline at 2020-11-22 23:59 (as discussed with stefaniebutland here). I am a bit early 😎 👍

I would enjoy some feedback on the post:

• I intend the blog post to be easy and informal (as I already have a more formal JOSS article). Did I succeed, or did I overdo it?
• I am unsure if how the Rmd file is processed. Will it be run on rOpenSci server (and have the figures generated then), or must I add these to the Pull Request as well?

Looking forward to hear your thought, Richel Bilderbeek

[steffilazerte]

Hello @richelbilderbeek,
Thank you for your blog post! It's a really interesting look at the elegant simplicity of the mcbette package.

I love your casual tone, it is a great way to write for this audience and makes it education AND fun :)

I have 25 specific inline comments (mostly minor typos and stylistic things) and a couple of other, 'broader' suggestions:

• You do need to compile your index.Rmd file locally and then push the .md file and all associated figures (You can preview your blog post by clicking on the "Details" link next to the bottom "check" that talks about the "Preview ready". This opens a preview of the rOpenSci website, then just click on the "New" banner and you should see how your blog post will look once posted!)

• I would consider adding a small conclusion to the end of your section on mcbette that might lead into your section about the rOpenSci review process. Was there anything in particular that the reviewers suggested that was really helpful? It's also important to acknowledge the reviewers by name (and link to rOpenSci author page or GitHub page) and the review process (link to your review thread).

• My final 'big' comment is that it would be nice if your code was reproducible. Consider showing and adding brief explanations to bits of code that will help users set up what you've done and follow along with your examples.

Here are a couple of other things that we'll need before publishing. But we're almost there!

• post follows Content Guidelines
• post follows Style Guide
  • All package names should just be regular text (no backticks)
• title is in Title Case
• publication date is ok
  • December 1st 2020
• alternative text of images is informative
• Twitter metadata looks ok (paste post preview link in Twitter card validator; might have to click twice on "Preview card")
• author metadata is provided with correct folder name
  • I think you missed that section in the blog guide
• html not included in pull request of Rmd post
• I ran roblog::ro_lint_md() on index.md
  • I'll check when it's been reknit
• I ran roblog::ro_check_urls() on index.md
  • I'll check when it's been reknit
• I ran a spell-check on index.md
• YAML subject tags are ok
• YAML package-version included
• YAML subject tags - software peer review, packagename, R; add "community" for post by non-staff non-editor
• acknowledges and links to reviewers
• links to peer review thread

[steffilazerte]

Good place to acknowledge your reviewers and link to the review issue thread

[richelbilderbeek]

I now mention them. I think it is important to acknowledge them, yet I do feel this is a bit too much. Let me know what you think 👍

[richelbilderbeek]

Hi @steffilazerte, thanks for your awesome detailed feedback! I will process it before Sunday Nvember 22nd 23:59 👍

[richelbilderbeek]

Hi @steffilazerte,

As promised, I processed all your feedback. Thanks!

I do struggle most with getting the images right: I cannot see them on my own computer when adding the Hugo instructions to the R code block. Is there a way to be able to do so?

[steffilazerte]

Hi @richelbilderbeek,

To preview online look at the bottom of the Pull Request comments. you'll see a "All checks have passed" (or in the process of being checked) section. The final option in this list is the Preview. If you click on the "Details" link you'll open a preview of the rOpenSci blog (see screenshot, below). Right above the title ("Transforming science...") is a small banner that says "New! Selecting the Best Phylogenetic Evolutionary Model", click on that and you'll see the preview of your blog post!

Alternatively you can deploy the preview locally following these instructions.

Unfortunately looking at the documentation for par(), it seems as if mar is a parameter that can only be set with a call to par() (i.e. you can't include it as an argument).

I'll wait until you've had a chance to tweak things to your liking before I do the final once over. Thanks!

[steffilazerte]

Also to see just the images, you can look at the png file output in the folder, or run just the lines required to make the image:

library(beastier) # beastier is part of babette
fasta_filename <- tempfile("primates.fasta")
save_nexus_as_fasta(
  get_beast2_example_filename("Primates.nex"),
  fasta_filename
)

And then...

library(ape)
dna_sequences <- read.FASTA(fasta_filename)
image.DNAbin(dna_sequences, mar = c(15, 15, 3, 1))

[richelbilderbeek]

@steffilazerte: your help finding the completed doc was just what I needed. Thanks!

I will fix the technical problems before Wednesday Nov 24th 23:59 (Amsterdam time) 👍

[richelbilderbeek]

@steffilazerte I have processed all your feedback and checked the current preview. AFAICS it looks pretty. Thanks so much for your help!

Can you spot something else 👼 ?

[steffilazerte]

So close! It definitely looks beautiful :) The figures are lovely and nice and big now.
I have three final comments:

1. Please update the date of the folder to 2020-12-01
2. There is a kable() table that isn't being run, I just want to make sure that's what's intended (see my comment)
3. Please see my suggestion regarding the review thread and and the reviewers

Then we're done! Thank you for your patience!

[steffilazerte]

Link to the software review thread and to either rOpenSci author pages or link to GitHub
Was David Winter an official reviewer? From the review thread it looks like it was just Joëlle and Vikram...

Suggested change

	things in the process. My reviewers (@bjoelle, @dwinter and @vbaliga)
	things in the process. During the [rOpenSci review](https://github.com/ropensci/software-review/issues/360), my reviewers ([Joëlle Barido-Sottani](https://github.com/bjoelle), [David Winter](https://github.com/dwinter) and [Vikram Baliga](https://ropensci.org/author/vikram-b.-baliga/))

[richelbilderbeek]

Great suggestion! I used you suggestion literally in this commit.

[steffilazerte]

This isn't being run... should it be?

[richelbilderbeek]

Well spotted! It is run now 👍

[richelbilderbeek]

@steffilazerte I have processed the next wave of feedback. Thanks!

I cannot check the preview, however. Is this because the date is set to the future?

Well, maybe everything is OK now. Would be great 👍

[steffilazerte]

@richelbilderbeek It's not previewing because the index.md is missing... where'd it go?! Anything else and I would have made the fix for you but it'd probably be easiest if you compiled and uploaded the .md yourself.

This really should be the last change... thanks for your patience!

[richelbilderbeek]

@steffilazerte thanks! I thought it was just a temporary intermediate file. I've added it, but it does not look pretty yet. I will fix this within 31 hours (i.e. Friday 23:59) 👍

[richelbilderbeek]

@steffilazerte it took some tries, but everything works great now, at least, according to the preview! Do I overlook something or have we just finished this blog post?

[steffilazerte]

🎉 🎉 We're good to go! 🎉 🎉
I'm sure this took much longer than you envisioned, so I thank you for your patience and attention to detail.
The post looks great and is ready to be published on Tuesday. Get ready to bask in your glory 😉 !

[richelbilderbeek]

@steffilazerte 🥳 Thanks so much for your help! 🥳

[steffilazerte]

No need to respond unless you have suggestions or comments on this draft tweet announcing your blog post tomorrow.

Tweet draft:

---

[blog] Selecting the Best Phylogenetic Evolutionary Model

Richèl J.C. Bilderbeek (https://github.com/richelbilderbeek) demonstrates how R package mcbette (model comparisons using babette) addresses model selection in phylogeny.

https://ropensci.org/blog/2020/12/01/mcbette-selecting-the-best-inference-model/

#rstats #mcbette #babette

(1/2)

---

Shoutouts 🙏 to rOpenSci software reviewers Joëlle Barido-Sottani (https://github.com/bjoelle), @TheAtavism, and @labrichthys

(2/2)

[stefaniebutland]

@steffilazerte Vikram Baliga on twitter is @labrichthys https://twitter.com/labrichthys